https://docs.moodle.org/2x/pl/api.php?action=feedcontributions&feedformat=atom&user=Geoffr
MoodleDocs - Wkład użytkownika [pl]
2026-06-03T19:39:02Z
Wkład użytkownika
MediaWiki 1.43.5
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111518
Jmol Help
2014-03-30T20:59:22Z
<p>Geoffr: /* Jmol measurements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom<br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom<br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
== Jmol default colours ==<br />
=== Elements: CPK colour scheme ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td title="110 Ds Darmstadtium" bgcolor="#eb0026">Ds</td><br />
<td title="111 Rg Roentgenium" bgcolor="#eb0026">Rg</td><br />
<td title="112 Cn Copernicium" bgcolor="#eb0026">Cn</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues: Amino colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
</table><br />
===== Amino acid residues: Shapely colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide base residues: Shapely colour scheme =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111517
Jmol Help
2014-03-30T20:58:11Z
<p>Geoffr: </p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
== Jmol default colours ==<br />
=== Elements: CPK colour scheme ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td title="110 Ds Darmstadtium" bgcolor="#eb0026">Ds</td><br />
<td title="111 Rg Roentgenium" bgcolor="#eb0026">Rg</td><br />
<td title="112 Cn Copernicium" bgcolor="#eb0026">Cn</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues: Amino colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
</table><br />
===== Amino acid residues: Shapely colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide base residues: Shapely colour scheme =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111516
Jmol Help
2014-03-30T20:45:57Z
<p>Geoffr: /* Elements: CPK colour scheme */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements: CPK colour scheme ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td title="110 Ds Darmstadtium" bgcolor="#eb0026">Ds</td><br />
<td title="111 Rg Roentgenium" bgcolor="#eb0026">Rg</td><br />
<td title="112 Cn Copernicium" bgcolor="#eb0026">Cn</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues: Amino colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
</table><br />
===== Amino acid residues: Shapely colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide base residues: Shapely colour scheme =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111515
Jmol Help
2014-03-30T20:36:41Z
<p>Geoffr: /* Elements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements: CPK colour scheme ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues: Amino colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
</table><br />
===== Amino acid residues: Shapely colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide base residues: Shapely colour scheme =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111514
Jmol Help
2014-03-30T20:31:06Z
<p>Geoffr: /* Nucleotide base residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues: Amino colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
</table><br />
===== Amino acid residues: Shapely colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide base residues: Shapely colour scheme =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111513
Jmol Help
2014-03-30T20:30:14Z
<p>Geoffr: /* Amino acid residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues: Amino colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
</table><br />
===== Amino acid residues: Shapely colour scheme =====<br />
<table style="text-align: center;"><br />
<tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide base residues =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111512
Jmol Help
2014-03-30T20:26:51Z
<p>Geoffr: /* Nucleotide_base_residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide base residues =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111511
Jmol Help
2014-03-30T20:24:07Z
<p>Geoffr: /* Amino acid residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx<br />
</td><br />
</tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide_base_residues =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111510
Jmol Help
2014-03-30T20:20:00Z
<p>Geoffr: /* Amino acid residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #C8C8C8;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #145AFF;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00DCDC;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #E6E600;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #00DCDC;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #8282D2;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #0F820F;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #0F820F;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #145AFF;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #E6E600;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #3232AA;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #DC9682;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FA9600;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #FA9600;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #B45AB4;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #3232AA;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #0F820F;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #BEA06E;"> Xxx<br />
</td><br />
</tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide_base_residues =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111509
Jmol Help
2014-03-30T20:11:44Z
<p>Geoffr: /* Amino acid residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
<tr></tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
<br />
===== Nucleotide_base_residues =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111508
Jmol Help
2014-03-30T20:09:42Z
<p>Geoffr: /* Amino acid residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
<tr></tr><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td><br />
</tr><br />
</table><br />
===== Nucleotide_base_residues =====<br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111507
Jmol Help
2014-03-30T20:03:23Z
<p>Geoffr: /* Polypeptides, nucleic acids and carbohydrates */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111506
Jmol Help
2014-03-30T20:02:35Z
<p>Geoffr: /* Secondary structure */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates =====<br />
<table><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111505
Jmol Help
2014-03-30T20:02:03Z
<p>Geoffr: /* Secondary structure */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
===== Polypeptides, nucleic acids and carbohydrates<br />
<table><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111504
Jmol Help
2014-03-30T19:59:34Z
<p>Geoffr: /* Elements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">Polypeptides</td><br />
<td></td><br />
<td colspan="3">Nucleic acids</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111503
Jmol Help
2014-03-30T19:57:51Z
<p>Geoffr: /* Amino acid residues */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
<br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">Polypeptides</td><br />
<td></td><br />
<td colspan="3">Nucleic acids</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111502
Jmol Help
2014-03-30T19:56:51Z
<p>Geoffr: /* Elements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals" style="width: 2em">1</th><br />
<th title="Group2, the alkaline earth metals" style="width: 2em">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th><br />
<th title="Group4, the titanium group" style="width: 2em">4</th><br />
<th title="Group5, the vanadium group" style="width: 2em">5</th><br />
<th title="Group6, the chromium group" style="width: 2em">6</th><br />
<th title="Group7, the manganese group" style="width: 2em">7</th><br />
<th title="Group8, the iron group" style="width: 2em">8</th><br />
<th title="Group9, the cobalt group" style="width: 2em">9</th><br />
<th title="Group10, the nickel group" style="width: 2em">10</th><br />
<th title="Group11, the copper group, coinage metals" style="width: 2em">11</th><br />
<th title="Group12, the zinc group" style="width: 2em">12</th><br />
<th title="Group13, the boron group" style="width: 2em">13</th><br />
<th title="Group14, the carbon group" style="width: 2em">14</th><br />
<th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th><br />
<th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th><br />
<th title="Group17, the halogens" style="width: 2em">17</th><br />
<th title="Group18, the noble gases" style="width: 2em">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">Polypeptides</td><br />
<td></td><br />
<td colspan="3">Nucleic acids</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111501
Jmol Help
2014-03-30T19:53:18Z
<p>Geoffr: /* Elements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals">1</th><br />
<th title="Group2, the alkaline earth metals">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids">3</th><br />
<th title="Group4, the titanium group ">4</th><br />
<th title="Group5, the vanadium group ">5</th><br />
<th title="Group6, the chromium group ">6</th><br />
<th title="Group7, the manganese group ">7</th><br />
<th title="Group8, the iron group ">8</th><br />
<th title="Group9, the cobalt group ">9</th><br />
<th title="Group10, the nickel group ">10</th><br />
<th title="Group11, the copper group, coinage metals ">11</th><br />
<th title="Group12, the zinc group ">12</th><br />
<th title="Group13, the boron group">13</th><br />
<th title="Group14, the carbon group">14</th><br />
<th title="Group15, the pnictogens, nitrogen group">15</th><br />
<th title="Group16, the chalcogens, oxygen group">16</th><br />
<th title="Group17, the halogens">17</th><br />
<th title="Group18, the noble gases">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ffffff">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">Polypeptides</td><br />
<td></td><br />
<td colspan="3">Nucleic acids</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111500
Jmol Help
2014-03-30T19:52:16Z
<p>Geoffr: /* Elements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<th title="Group1, the alkali metals">1</th><br />
<th title="Group2, the alkaline earth metals">2</th><br />
<th title="Group3, the scandium group including the lanthanoids and actinoids">3</th><br />
<th title="Group4, the titanium group ">4</th><br />
<th title="Group5, the vanadium group ">5</th><br />
<th title="Group6, the chromium group ">6</th><br />
<th title="Group7, the manganese group ">7</th><br />
<th title="Group8, the iron group ">8</th><br />
<th title="Group9, the cobalt group ">9</th><br />
<th title="Group10, the nickel group ">10</th><br />
<th title="Group11, the copper group, coinage metals ">11</th><br />
<th title="Group12, the zinc group ">12</th><br />
<th title="Group13, the boron group">13</th><br />
<th title="Group14, the carbon group">14</th><br />
<th title="Group15, the pnictogens, nitrogen group">15</th><br />
<th title="Group16, the chalcogens, oxygen group">16</th><br />
<th title="Group17, the halogens">17</th><br />
<th title="Group18, the noble gases">18</th><br />
</tr><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">Polypeptides</td><br />
<td></td><br />
<td colspan="3">Nucleic acids</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111499
Jmol Help
2014-03-30T19:48:59Z
<p>Geoffr: /* Elements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="width: 1em; background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="width: 1em; background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="width: 1em; background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="width: 1em; background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">Polypeptides</td><br />
<td></td><br />
<td colspan="3">Nucleic acids</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111498
Jmol Help
2014-03-30T19:44:25Z
<p>Geoffr: /* Secondary structure */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">Polypeptides</td><br />
<td></td><br />
<td colspan="3">Nucleic acids</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td><br />
</tr><br />
</table><br />
<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111497
Jmol Help
2014-03-30T19:38:51Z
<p>Geoffr: /* Polypeptides */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
<br />
<table><br />
<tr><br />
<td colspan="6">===== Polypeptides =====</td><br />
</tr><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td></tr></table><br />
<br />
===== Nucleic acids =====<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111496
Jmol Help
2014-03-30T19:34:55Z
<p>Geoffr: /* Polypeptides */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
===== Polypeptides =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td></tr></table><br />
<br />
===== Nucleic acids =====<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111495
Jmol Help
2014-03-30T19:34:11Z
<p>Geoffr: /* Secondary structure */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
==== Secondary structure ====<br />
===== Polypeptides =====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbo<wbr>hydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td></tr></table><br />
===== Nucleic acids =====<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111494
Jmol Help
2014-03-30T19:31:58Z
<p>Geoffr: </p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
=== Secondary structure ===<br />
==== Polypeptides ====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbo<wbr>hydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td></tr></table><br />
===== Nucleic acids =====<br />
==== Tertiary structure ====<br />
===== Polypeptides and nucleic acids =====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111493
Jmol Help
2014-03-30T19:29:09Z
<p>Geoffr: /* Biological macromolecules */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
=== Biological macromolecules ===<br />
==== Primary structure ====<br />
===== Amino acid residues =====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
=== Secondary structure ===<br />
==== Polypeptides ====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbo<wbr>hydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td></tr></table><br />
===== Nucleic acids =====<br />
=== Tertiary structure ===<br />
==== Polypeptides and nucleic acids ====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111492
Jmol Help
2014-03-30T19:27:53Z
<p>Geoffr: /* Jmol default element colours */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default colours ==<br />
=== Elements ===<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Biological macromolecules ==<br />
=== Primary structure ===<br />
==== Amino acid residues ====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
=== Secondary structure ===<br />
==== Polypeptides ====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbo<wbr>hydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td></tr></table><br />
==== Nucleic acids ====<br />
=== Tertiary structure ===<br />
==== Polypeptides and nucleic acids ====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111491
Jmol Help
2014-03-30T19:02:12Z
<p>Geoffr: /* Jmol measurements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Biological macromolecules ==<br />
=== Primary structure ===<br />
==== Amino acid residues ====<br />
<table style="text-align: center;"><br />
<tr><br />
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala<br />
</td><br />
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg<br />
</td><br />
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn<br />
</td><br />
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp<br />
</td><br />
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys<br />
</td><br />
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln<br />
</td><br />
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu<br />
</td><br />
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly<br />
</td><br />
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His<br />
</td><br />
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile<br />
</td><br />
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu<br />
</td><br />
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys<br />
</td><br />
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met<br />
</td><br />
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe<br />
</td><br />
<td title="proline" style="width: 2em; background-color: #525252;"> Pro<br />
</td><br />
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser<br />
</td><br />
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr<br />
</td><br />
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp<br />
</td><br />
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr<br />
</td><br />
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val<br />
</td><br />
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx<br />
</td><br />
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx<br />
</td><br />
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx<br />
</td></tr></table><br />
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5><br />
<table><br />
<tr><br />
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A<br />
</td><br />
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G<br />
</td><br />
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I<br />
</td><br />
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C<br />
</td><br />
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T<br />
</td><br />
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U<br />
</td></tr></table><br />
=== Secondary structure ===<br />
==== Polypeptides ====<br />
<table><br />
<tr><br />
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix<br />
</td><br />
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix<br />
</td><br />
<td style="width:5em; background-color: #600080; text-align: center;">π helix<br />
</td><br />
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand<br />
</td><br />
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA<br />
</td><br />
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other<br />
</td><br />
<td style="width:5em; background-color: #FFFFFF; text-align: center;"><br />
</td><br />
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbo<wbr>hydrate<br />
</td><br />
<td style="width:5em; background-color: #808080; text-align: center;">other<br />
</td></tr></table><br />
==== Nucleic acids ====<br />
=== Tertiary structure ===<br />
==== Polypeptides and nucleic acids ====<br />
<br />
<table style="border-spacing:0;border-collapse:collapse"><br />
<tr><br />
<td colspan="16" style="text-align:left">N-terminal or 5’-<br />
</td><br />
<td><br />
</td><br />
<td colspan="16" style="text-align:right">C-terminal or 3’-<br />
</td></tr><br />
<tr style="height:1em"><br />
<td style="width:1em; background-color:#0000ff"><br />
</td><br />
<td style="width:1em; background-color:#0020ff"><br />
</td><br />
<td style="width:1em; background-color:#0040ff"><br />
</td><br />
<td style="width:1em; background-color:#0060ff"><br />
</td><br />
<td style="width:1em; background-color:#0080ff"><br />
</td><br />
<td style="width:1em; background-color:#00a0ff"><br />
</td><br />
<td style="width:1em; background-color:#00c0ff"><br />
</td><br />
<td style="width:1em; background-color:#00e0ff"><br />
</td><br />
<td style="width:1em; background-color:#00ffff"><br />
</td><br />
<td style="width:1em; background-color:#00ffe0"><br />
</td><br />
<td style="width:1em; background-color:#00ffc0"><br />
</td><br />
<td style="width:1em; background-color:#00ffa0"><br />
</td><br />
<td style="width:1em; background-color:#00ff80"><br />
</td><br />
<td style="width:1em; background-color:#00ff60"><br />
</td><br />
<td style="width:1em; background-color:#00ff40"><br />
</td><br />
<td style="width:1em; background-color:#00ff20"><br />
</td><br />
<td style="width:1em; background-color:#00ff00"><br />
</td><br />
<td style="width:1em; background-color:#20ff00"><br />
</td><br />
<td style="width:1em; background-color:#40ff00"><br />
</td><br />
<td style="width:1em; background-color:#60ff00"><br />
</td><br />
<td style="width:1em; background-color:#80ff00"><br />
</td><br />
<td style="width:1em; background-color:#a0ff00"><br />
</td><br />
<td style="width:1em; background-color:#c0ff00"><br />
</td><br />
<td style="width:1em; background-color:#e0ff00"><br />
</td><br />
<td style="width:1em; background-color:#ffff00"><br />
</td><br />
<td style="width:1em; background-color:#ffe000"><br />
</td><br />
<td style="width:1em; background-color:#ffc000"><br />
</td><br />
<td style="width:1em; background-color:#ffa000"><br />
</td><br />
<td style="width:1em; background-color:#ff8000"><br />
</td><br />
<td style="width:1em; background-color:#ff6000"><br />
</td><br />
<td style="width:1em; background-color:#ff4000"><br />
</td><br />
<td style="width:1em; background-color:#ff2000"><br />
</td><br />
<td style="width:1em; background-color:#ff0000"><br />
</td></tr></table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111490
Jmol Help
2014-03-30T15:34:46Z
<p>Geoffr: /* More */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111489
Jmol Help
2014-03-30T15:34:20Z
<p>Geoffr: /* More */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see:<br />
[http://jmol.sourceforge.net Jmol]<br />
[http://wiki.jmol.org Jmol Wiki]<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111488
Jmol Help
2014-03-30T15:33:38Z
<p>Geoffr: /* More */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: <br />
<br />
[http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111487
Jmol Help
2014-03-30T15:32:44Z
<p>Geoffr: /* More */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: <br />
<br />
[http://jmol.sourceforge.net http://jmol.sourceforge.net Jmol]<br />
<br />
[http://wiki.jmol.org Jmol Wiki]<br />
<br />
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111486
Jmol Help
2014-03-30T15:31:53Z
<p>Geoffr: /* More */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: <br />
<br />
[[http://jmol.sourceforge.net http://jmol.sourceforge.net Jmol]]<br />
[[http://wiki.jmol.org Jmol Wiki]]<br />
[[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111485
Jmol Help
2014-03-30T15:31:07Z
<p>Geoffr: /* More */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: <br />
[[http://jmol.sourceforge.net http://jmol.sourceforge.net] Jmol]<br />
[[http://wiki.jmol.org Jmol Wiki]]<br />
[[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111484
Jmol Help
2014-03-30T15:17:56Z
<p>Geoffr: /* Jmol default element colours */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111483
Jmol Help
2014-03-30T15:11:49Z
<p>Geoffr: /* Jmol measurements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
== Jmol measurements ==<br />
* Distance between 2 atoms:<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle between 3 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral between 4 atoms:<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111482
Jmol Help
2014-03-30T15:09:17Z
<p>Geoffr: /* Jmol mouse control */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
== Jmol measurements ==<br />
* Distance (2 atoms):<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle (3 atoms):<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral (4 atoms)<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111481
Jmol Help
2014-03-30T15:08:34Z
<p>Geoffr: </p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
== Jmol measurements ==<br />
* Distance (2 atoms):<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle (3 atoms):<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral (4 atoms)<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111480
Jmol Help
2014-03-30T15:06:38Z
<p>Geoffr: /* Jmol mouse control */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table style="text-align: left"><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance (2 atoms):<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle (3 atoms):<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral (4 atoms)<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111479
Jmol Help
2014-03-30T15:04:34Z
<p>Geoffr: /* Jmol measurements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance (2 atoms):<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle (3 atoms):<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral (4 atoms)<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111478
Jmol Help
2014-03-30T15:03:37Z
<p>Geoffr: /* Jmol measurements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance (2 atoms):<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle (3 atoms):<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral (4 atoms)<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
<br />
* In all cases:<br />
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
** move outside the window in order to cancel the measurement<br />
** make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111477
Jmol Help
2014-03-30T15:01:27Z
<p>Geoffr: /* Jmol measurements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
* Distance (2 atoms):<br />
# double-click on the starting atom<br />
# to fix a distance measurement, double-click on second atom</p><br />
<br />
* Angle (3 atoms):<br />
# double-click on the starting atom<br />
# click on the second atom (central atom in angle)<br />
# to fix an angle measurement, double-click on third atom</p><br />
<br />
* Torsion angle or dihedral (4 atoms)<br />
# double-click on the starting atom<br />
# click on the second atom<br />
# click on the third atom</p><br />
# to fix a dihedral angle measurement, double-click on fourth atom<br />
* In all cases:<br />
* move pointer over destination atom in order to see measurement results without leaving a permanent measurement <br />
* move outside the window in order to cancel the measurement<br />
* make the same measurement again in order to delete the measurement<br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111476
Jmol Help
2014-03-30T14:55:14Z
<p>Geoffr: /* Jmol measurements */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
<br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111475
Jmol Help
2014-03-30T14:51:53Z
<p>Geoffr: /* Jmol mouse control */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<th>Jmol menu</th><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<th>Rotate X,Y</th><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Translate X,Y</th><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<th>Rotate Z</th><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<th>Zoom </th><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Reset &amp; centre</th><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<th>Resize Jmol</th><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111474
Jmol Help
2014-03-30T14:49:18Z
<p>Geoffr: /* Jmol mouse control */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<td>Jmol menu</td><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<td>Rotate X,Y</td><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Translate X,Y</td><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<td>Rotate Z</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<td>Zoom </td><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Reset &amp; centre</td><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Resize Jmol</td><br />
<td>Click &amp; drag bottom-right corner</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111473
Jmol Help
2014-03-30T14:45:53Z
<p>Geoffr: /* Jmol default element colours */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<td>Jmol menu</td><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<td>Rotate X,Y</td><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Translate X,Y</td><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<td>Rotate Z</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<td>Zoom </td><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Reset &amp; centre</td><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111472
Jmol Help
2014-03-30T14:45:11Z
<p>Geoffr: /* Jmol default element colours */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table style="text-align:center"><br />
<tr style="text-align:center"><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<td>Jmol menu</td><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<td>Rotate X,Y</td><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Translate X,Y</td><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<td>Rotate Z</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<td>Zoom </td><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Reset &amp; centre</td><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111471
Jmol Help
2014-03-30T14:44:31Z
<p>Geoffr: /* Jmol default element colours */</p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table><br />
<tr style="text-align:center"><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<td>Jmol menu</td><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<td>Rotate X,Y</td><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Translate X,Y</td><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<td>Rotate Z</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<td>Zoom </td><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Reset &amp; centre</td><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111470
Jmol Help
2014-03-30T14:40:24Z
<p>Geoffr: </p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<td>Jmol menu</td><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<td>Rotate X,Y</td><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Translate X,Y</td><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<td>Rotate Z</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<td>Zoom </td><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Reset &amp; centre</td><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
==More==<br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr
https://docs.moodle.org/2x/pl/index.php?title=Jmol_Help&diff=111469
Jmol Help
2014-03-30T14:39:10Z
<p>Geoffr: </p>
<hr />
<div>Help with using the [[Jmol_filter]]<br />
== Jmol default element colours ==<br />
Hover over any element to see more information (Atomic Number, Symbol, Element Name)<br />
<table><br />
<tr><br />
<td title="1 H Hydrogen" style="background-color:#ff0000">H</td><br />
<td rowspan="1" colspan="16"></td><br />
<td title="2 He Helium" style="background-color:#d9ffff">He</td><br />
</tr><br />
<tr><br />
<td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td><br />
<td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td><br />
<td colspan="10"></td><br />
<td title="5 B Boron" bgcolor="#ffb5b5">B</td><br />
<td title="6 C Carbon" bgcolor="#909090">C</td><br />
<td title="7 N Nitrogen" bgcolor="#3050f8">N</td><br />
<td title="8 O Oxygen" bgcolor="#ff0d0d">O</td><br />
<td title="9 F Fluorine" bgcolor="#90e050">F</td><br />
<td title="10 Ne Neon" bgcolor="#b3e3f5">Ne</td><br />
</tr><br />
<tr><br />
<td title="11 Na Sodium" bgcolor="#ab5cf2">Na</td><br />
<td title="12 Mg Magnesium" bgcolor="#8aff00">Mg</td><br />
<td colspan="10"></td><br />
<td title="13 Al Aluminium" bgcolor="#bfa6a6">Al</td><br />
<td title="14 Si Silicon" bgcolor="#f0c8a0">Si</td><br />
<td title="15 P Phosphorus" bgcolor="#ff8000">P</td><br />
<td title="16 S Sulphur" bgcolor="#ffff30">S</td><br />
<td title="17 Cl Chlorine" bgcolor="#1ff01f">Cl</td><br />
<td title="18 Ar Argon" bgcolor="#80d1e3">Ar</td><br />
</tr><br />
<tr><br />
<td title="19 K Potassium" bgcolor="#8f40d4">K</td><br />
<td title="20 Ca Calcium" bgcolor="#3dff00">Ca</td><br />
<td title="21 Sc Scandium" bgcolor="#e6e6e6">Sc</td><br />
<td title="22 Ti Titanium" bgcolor="#bfc2c7">Ti</td><br />
<td title="23 V Vanadium" bgcolor="#a6a6ab">V</td><br />
<td title="24 Cr Chromium" bgcolor="#8a99c7">Cr</td><br />
<td title="25 Mn Manganese" bgcolor="#9c7ac7">Mn</td><br />
<td title="26 Fe Iron" bgcolor="#e06633">Fe</td><br />
<td title="27 Co Cobalt" bgcolor="#f090a0">Co</td><br />
<td title="28 Ni Nickel" bgcolor="#50d050">Ni</td><br />
<td title="29 Cu Copper" bgcolor="#c88033">Cu</td><br />
<td title="30 Zn Zinc" bgcolor="#7d80b0">Zn</td><br />
<td title="31 Ga Gallium" bgcolor="#c28f8f">Ga</td><br />
<td title="32 Ge Germanium" bgcolor="#668f8f">Ge</td><br />
<td title="33 As Arsenic" bgcolor="#bd80e3">As</td><br />
<td title="34 Se Selenium" bgcolor="#ffa100">Se</td><br />
<td title="35 Br Bromine" bgcolor="#a62929">Br</td><br />
<td title="36 Kr Krypton" bgcolor="#5cb8d1">Kr</td><br />
</tr><br />
<tr><br />
<td title="37 Rb Rubidium" bgcolor="#702eb0">Rb</td><br />
<td title="38 Sr Strontium" bgcolor="#00ff00">Sr</td><br />
<td title="39 Y Yttrium" bgcolor="#94ffff">Y</td><br />
<td title="40 Zr Zirconium" bgcolor="#94e0e0">Zr</td><br />
<td title="41 Nb Niobium" bgcolor="#73c2c9">Nb</td><br />
<td title="42 Mo Molybdenum" bgcolor="#54b5b5">Mo</td><br />
<td title="43 Tc Technetium" bgcolor="#3b9e9e">Tc</td><br />
<td title="44 Ru Ruthenium" bgcolor="#248f8f">Ru</td><br />
<td title="45 Rh Rhodium" bgcolor="#0a7d8c">Rh</td><br />
<td title="46 Pd Palladium" bgcolor="#006985">Pd</td><br />
<td title="47 Ag Silver" bgcolor="#c0c0c0">Ag</td><br />
<td title="48 Cd Cadmium" bgcolor="#ffd98f">Cd</td><br />
<td title="49 In Indium" bgcolor="#a67573">In</td><br />
<td title="50 Sn Tin" bgcolor="#668080">Sn</td><br />
<td title="51 Sb Antimony" bgcolor="#9e63b5">Sb</td><br />
<td title="52 Te Tellerium" bgcolor="#d47a00">Te</td><br />
<td title="53 I Iodine" bgcolor="#940094">I</td><br />
<td title="54 Xe Xenon" bgcolor="#429eb0">Xe</td><br />
</tr><br />
<tr><br />
<td title="55 Cs Caesium" bgcolor="#57178f">Cs</td><br />
<td title="56 Ba Barium" bgcolor="#00c900">Ba</td><br />
<td>*</td><br />
<td title="72 Hf Hafnium" bgcolor="#4dc2ff">Hf</td><br />
<td title="73 Ta Tantalum" bgcolor="#4da6ff">Ta</td><br />
<td title="74 W Tungsten" bgcolor="#2194d6">W</td><br />
<td title="75 Re Rhenium" bgcolor="#267dab">Re</td><br />
<td title="76 Os Osmium" bgcolor="#266696">Os</td><br />
<td title="77 Ir Iridium" bgcolor="#175487">Ir</td><br />
<td title="78 Pt Platinum" bgcolor="#d0d0e0">Pt</td><br />
<td title="79 Au Gold" bgcolor="#ffd123">Au</td><br />
<td title="80 Hg Mercury" bgcolor="#b8b8d0">Hg</td><br />
<td title="81 Tl Thallium" bgcolor="#a6544d">Tl</td><br />
<td title="82 Pb Lead" bgcolor="#575961">Pb</td><br />
<td title="83 Bi Bismuth" bgcolor="#9e4fb5">Bi</td><br />
<td title="84 Po Polonium" bgcolor="#ab5c00">Po</td><br />
<td title="85 At Astatine" bgcolor="#754f45">At</td><br />
<td title="86 Rn Radon" bgcolor="#428296">Rn</td><br />
</tr><br />
<tr><br />
<td title="87 Fr Francium" bgcolor="#420066">Fr</td><br />
<td title="88 Ra Radium" bgcolor="#007d00">Ra</td><br />
<td>**</td><br />
<td title="104 Rf Rutherfordium" bgcolor="#cc0059">Rf</td><br />
<td title="105 Db Dubnium" bgcolor="#d1004f">Db</td><br />
<td title="106 Sg Seaborgium" bgcolor="#d90045">Sg</td><br />
<td title="107 Bh Bohrium" bgcolor="#e00038">Bh</td><br />
<td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td><br />
<td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td colspan="18">&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>*</td><br />
<td title="57 La Lanthanum" bgcolor="#70d4ff">La</td><br />
<td title="58 Ce Cerium" bgcolor="#ffffc7">Ce</td><br />
<td title="59 Pr Praseodymium" bgcolor="#d9ffc7">Pr</td><br />
<td title="60 Nd Neodymium" bgcolor="#c7ffc7">Nd</td><br />
<td title="61 Pm Promethium" bgcolor="#a3ffc7">Pm</td><br />
<td title="62 Sm Samarium" bgcolor="#8fffc7">Sm</td><br />
<td title="63 Eu Europium" bgcolor="#61ffc7">Eu</td><br />
<td title="64 Gd Gadolinium" bgcolor="#45ffc7">Gd</td><br />
<td title="65 Tb Terbium" bgcolor="#30ffc7">Tb</td><br />
<td title="66 Dy Dysprosium" bgcolor="#1fffc7">Dy</td><br />
<td title="67 Ho Holmium" bgcolor="#00ff9c">Ho</td><br />
<td title="68 Er Erbium" bgcolor="#00e675">Er</td><br />
<td title="69 Tm Thulium" bgcolor="#00d452">Tm</td><br />
<td title="70 Yb Ytterbium" bgcolor="#00bf38">Yb</td><br />
<td title="71 Lu Lutetium" bgcolor="#00ab24">Lu</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>&nbsp;</td><br />
<td>**</td><br />
<td title="89 Ac Actinium" bgcolor="#70abfa">Ac</td><br />
<td title="90 Th Thorium" bgcolor="#00baff">Th</td><br />
<td title="91 Pa Protoactinium" bgcolor="#00a1ff">Pa</td><br />
<td title="92 U Uranium" bgcolor="#008fff">U</td><br />
<td title="93 Np Neptunium" bgcolor="#0080ff">Np</td><br />
<td title="94 Pu Plutonium" bgcolor="#006bff">Pu</td><br />
<td title="95 Am Americium" bgcolor="#545cf2">Am</td><br />
<td title="96 Cm Curium" bgcolor="#785ce3">Cm</td><br />
<td title="97 Bk Berkelium" bgcolor="#8a4fe3">Bk</td><br />
<td title="98 Cf Californium" bgcolor="#a136d4">Cf</td><br />
<td title="99 Es Einsteinium" bgcolor="#b31fd4">Es</td><br />
<td title="100 Fm Fermium" bgcolor="#b31fba">Fm</td><br />
<td title="101 Md Mendelevium" bgcolor="#b30da6">Md</td><br />
<td title="102 No Nobelium" bgcolor="#bd0d87">No</td><br />
<td title="103 Lr Lawrencium" bgcolor="#c70066">Lr</td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
== Jmol mouse control ==<br />
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.<br />
<table><br />
<tr><br />
<th>Action</th><br />
<th>Main (left) button</th><br />
<th>Middle button</th><br />
<th>Secondary (right) button</th><br />
</tr><br />
<tr><br />
<td>Jmol menu</td><br />
<td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td><br />
<td>&nbsp;</td><br />
<td>Click</td><br />
</tr><br />
<tr><br />
<td>Rotate X,Y</td><br />
<td>Click &amp; drag</td><br />
<td>&nbsp;</td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Translate X,Y</td><br />
<td>Shift + double-click &amp; drag</td><br />
<td>Double-click &amp; drag</td><br />
<td>Ctrl + click &amp; drag</td><br />
</tr><br />
<tr><br />
<td>Rotate Z</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
<td>Click &amp; drag horizontally</td><br />
<td>Shift + click &amp; drag horizontally</td><br />
</tr><br />
<tr><br />
<td>Zoom </td><br />
<td>Shift + click &amp; drag vertically</td><br />
<td>Click &amp; drag vertically<br><br />
<span style="font-style: italic;">or</span> mouse wheel </td><br />
<td>&nbsp;</td><br />
</tr><br />
<tr><br />
<td>Reset &amp; centre</td><br />
<td>Shift + double-click (away from molecule)</td><br />
<td>Double-click (away from molecule) </td><br />
<td>&nbsp;</td><br />
</tr><br />
</table><br />
<br />
== Jmol measurements ==<br />
<ul><br />
<li><br />
<p> Distance (2 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>to fix a distance measurement, double-click on second atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Angle (3 atoms):</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom (central atom in angle) </p><br />
</li><br />
<li><br />
<p>to fix an angle measurement, double-click on third atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> Torsion angle or dihedral (4 atoms)</p><br />
<ol type="1"><br />
<li><br />
<p>double-click on the starting atom</p><br />
</li><br />
<li><br />
<p>click on the second atom</p><br />
</li><br />
<li><br />
<p>click on the third atom</p><br />
</li><br />
<li><br />
<p>to fix a dihedral angle measurement, double-click on fourth atom</p><br />
</li><br />
</ol><br />
</li><br />
<li><br />
<p> In all cases:</p><br />
<ul><br />
<li><br />
<p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p><br />
</li><br />
<li><br />
<p> move outside the window in order to cancel the measurement</p><br />
</li><br />
<li><br />
<p> make the same measurement again in order to delete the measurement</p><br />
</li><br />
</ul><br />
</li><br />
</ul><br />
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]</div>
Geoffr