Difference between revisions of "Jmol Help"

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Help with using the [[Jmol_filter]]
 
Help with using the [[Jmol_filter]]
== Jmol default element colours ==
+
== Jmol mouse control ==
 +
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.
 +
<table style="text-align: left">
 +
    <tr>
 +
      <th>Action</th>
 +
      <th>Main (left) button</th>
 +
      <th>Middle button</th>
 +
      <th>Secondary (right) button</th>
 +
    </tr>
 +
    <tr>
 +
      <th>Jmol menu</th>
 +
      <td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td>
 +
      <td>&nbsp;</td>
 +
      <td>Click</td>
 +
    </tr>
 +
    <tr>
 +
      <th>Rotate X,Y</th>
 +
      <td>Click &amp; drag</td>
 +
      <td>&nbsp;</td>
 +
      <td>&nbsp;</td>
 +
    </tr>
 +
    <tr>
 +
      <th>Translate X,Y</th>
 +
      <td>Shift + double-click &amp; drag</td>
 +
      <td>Double-click &amp; drag</td>
 +
      <td>Ctrl + click &amp; drag</td>
 +
    </tr>
 +
    <tr>
 +
      <th>Rotate Z</th>
 +
      <td>Shift + click &amp; drag horizontally</td>
 +
      <td>Click &amp; drag horizontally</td>
 +
      <td>Shift + click &amp; drag horizontally</td>
 +
    </tr>
 +
    <tr>
 +
      <th>Zoom </th>
 +
      <td>Shift + click &amp; drag vertically</td>
 +
      <td>Click &amp; drag vertically<br>
 +
      <span style="font-style: italic;">or</span> mouse wheel </td>
 +
      <td>&nbsp;</td>
 +
    </tr>
 +
    <tr>
 +
      <th>Reset &amp; centre</th>
 +
      <td>Shift + double-click (away from molecule)</td>
 +
      <td>Double-click (away from molecule) </td>
 +
      <td>&nbsp;</td>
 +
    </tr>
 +
    <tr>
 +
      <th>Resize Jmol</th>
 +
      <td>Click &amp; drag bottom-right corner</td>
 +
      <td>&nbsp;</td>
 +
      <td>&nbsp;</td>
 +
    </tr>
 +
</table>
 +
 
 +
== Jmol measurements ==
 +
* Distance between 2 atoms:
 +
# double-click on the starting atom
 +
# to fix a distance measurement, double-click on second atom
 +
   
 +
* Angle between 3 atoms:
 +
# double-click on the starting atom
 +
# click on the second atom (central atom in angle)
 +
# to fix an angle measurement, double-click on third atom
 +
 
 +
* Torsion angle or dihedral between 4 atoms:
 +
# double-click on the starting atom
 +
# click on the second atom
 +
# click on the third atom</p>
 +
# to fix a dihedral angle measurement, double-click on fourth atom
 +
 
 +
* In all cases:
 +
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement 
 +
** move outside the window in order to cancel the measurement
 +
** make the same measurement again in order to delete the measurement
 +
 
 +
== Jmol default colours ==
 +
=== Elements: CPK colour scheme ===
 
Hover over any element to see more information (Atomic Number, Symbol, Element Name)
 
Hover over any element to see more information (Atomic Number, Symbol, Element Name)
 
<table style="text-align:center">
 
<table style="text-align:center">
 
     <tr>
 
     <tr>
       <td title="1 H Hydrogen" style="background-color:#ff0000">H</td>
+
    <th title="Group1, the alkali metals" style="width: 2em">1</th>
 +
    <th title="Group2, the alkaline earth metals" style="width: 2em">2</th>
 +
    <th title="Group3, the scandium group including the lanthanoids and actinoids" style="width: 2em">3</th>
 +
    <th title="Group4, the titanium group" style="width: 2em">4</th>
 +
    <th title="Group5, the vanadium group" style="width: 2em">5</th>
 +
    <th title="Group6, the chromium group" style="width: 2em">6</th>
 +
    <th title="Group7, the manganese group" style="width: 2em">7</th>
 +
    <th title="Group8, the iron group" style="width: 2em">8</th>
 +
    <th title="Group9, the cobalt group" style="width: 2em">9</th>
 +
    <th title="Group10, the nickel group" style="width: 2em">10</th>
 +
    <th title="Group11, the copper group, coinage metals" style="width: 2em">11</th>
 +
    <th title="Group12, the zinc group" style="width: 2em">12</th>
 +
    <th title="Group13, the boron group" style="width: 2em">13</th>
 +
    <th title="Group14, the carbon group" style="width: 2em">14</th>
 +
    <th title="Group15, the pnictogens, nitrogen group" style="width: 2em">15</th>
 +
    <th title="Group16, the chalcogens, oxygen group" style="width: 2em">16</th>
 +
    <th title="Group17, the halogens" style="width: 2em">17</th>
 +
    <th title="Group18, the noble gases" style="width: 2em">18</th>
 +
    </tr>
 +
    <tr>
 +
       <td title="1 H Hydrogen" style="background-color:#ffffff; border:1px solid lightgray">H</td>
 
       <td rowspan="1" colspan="16"></td>
 
       <td rowspan="1" colspan="16"></td>
 
       <td title="2 He Helium" style="background-color:#d9ffff">He</td>
 
       <td title="2 He Helium" style="background-color:#d9ffff">He</td>
 
     </tr>
 
     </tr>
 
     <tr>
 
     <tr>
       <td title="3 Li Lithium" style="background-color:"#cc80ff">Li</td>
+
       <td title="3 Li Lithium" style="background-color:#cc80ff">Li</td>
 
       <td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td>
 
       <td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td>
 
       <td colspan="10"></td>
 
       <td colspan="10"></td>
Line 100: Line 196:
 
       <td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td>
 
       <td title="108 Hs Hassium" bgcolor="#e6002e">Hs</td>
 
       <td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td>
 
       <td title="109 Mt Meitnerium" bgcolor="#eb0026">Mt</td>
       <td>&nbsp;</td>
+
       <td title="110 Ds Darmstadtium" bgcolor="#eb0026">Ds</td>
       <td>&nbsp;</td>
+
       <td title="111 Rg Roentgenium" bgcolor="#eb0026">Rg</td>
       <td>&nbsp;</td>
+
       <td title="112 Cn Copernicium" bgcolor="#eb0026">Cn</td>
 
       <td>&nbsp;</td>
 
       <td>&nbsp;</td>
 
       <td>&nbsp;</td>
 
       <td>&nbsp;</td>
Line 155: Line 251:
 
</table>
 
</table>
  
== Jmol mouse control ==
+
=== Biological macromolecules ===
Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or wheel mice.
+
==== Primary structure ====
<table style="text-align: left">
+
===== Amino acid residues: Amino colour scheme =====
    <tr>
+
<table style="text-align: center;">
      <th>Action</th>
+
<tr>
      <th>Main (left) button</th>
+
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala
      <th>Middle button</th>
+
</td>
      <th>Secondary (right) button</th>
+
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg
    </tr>
+
</td>
    <tr>
+
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn
      <th>Jmol menu</th>
+
</td>
      <td>Click on Jmol logo<br><span style="font-style: italic;">or</span> Ctrl + click</td>
+
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp
      <td>&nbsp;</td>
+
</td>
      <td>Click</td>
+
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys
    </tr>
+
</td>
    <tr>
+
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln
      <th>Rotate X,Y</th>
+
</td>
      <td>Click &amp; drag</td>
+
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu
      <td>&nbsp;</td>
+
</td>
      <td>&nbsp;</td>
+
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly
    </tr>
+
</td>
    <tr>
+
<td title="histidine" style="width: 2em; background-color: #8282D2"> His
      <th>Translate X,Y</th>
+
</td>
      <td>Shift + double-click &amp; drag</td>
+
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile
      <td>Double-click &amp; drag</td>
+
</td>
      <td>Ctrl + click &amp; drag</td>
+
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu
    </tr>
+
</td>
    <tr>
+
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys
      <th>Rotate Z</th>
+
</td>
      <td>Shift + click &amp; drag horizontally</td>
+
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met
      <td>Click &amp; drag horizontally</td>
+
</td>
      <td>Shift + click &amp; drag horizontally</td>
+
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe
    </tr>
+
</td>
    <tr>
+
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro
      <th>Zoom </th>
+
</td>
      <td>Shift + click &amp; drag vertically</td>
+
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser
      <td>Click &amp; drag vertically<br>
+
</td>
      <span style="font-style: italic;">or</span> mouse wheel </td>
+
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr
      <td>&nbsp;</td>
+
</td>
    </tr>
+
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp
    <tr>
+
</td>
      <th>Reset &amp; centre</th>
+
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr
      <td>Shift + double-click (away from molecule)</td>
+
</td>
      <td>Double-click (away from molecule) </td>
+
<td title="valine" style="width: 2em; background-color: #0F820F"> Val
      <td>&nbsp;</td>
+
</td>
    </tr>
+
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx
    <tr>
+
</td>
      <th>Resize Jmol</th>
+
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx
      <td>Click &amp; drag bottom-right corner</td>
+
</td>
      <td>&nbsp;</td>
+
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx
      <td>&nbsp;</td>
+
</td>
    </tr>
+
</tr>
 +
</table>
 +
===== Amino acid residues: Shapely colour scheme =====
 +
<table style="text-align: center;">
 +
<tr>
 +
<tr>
 +
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala
 +
</td>
 +
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg
 +
</td>
 +
<td title="asparagine" style="width: 2em; background-color: #00A1FF;"> Asn
 +
</td>
 +
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp
 +
</td>
 +
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys
 +
</td>
 +
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln
 +
</td>
 +
<td title="glutamic acid" style="width: 2em; background-color: #FF4C4C;"> Glu
 +
</td>
 +
<td title="glycine" style="width: 2em; background-color: #FFFFFF; border:1px solid lightgray;"> Gly
 +
</td>
 +
<td title="histidine" style="width: 2em; background-color: #7070FF;"> His
 +
</td>
 +
<td title="isoleucine" style="width: 2em; background-color: #004C00;"> Ile
 +
</td>
 +
<td title="leucine" style="width: 2em; background-color: #455E45;"> Leu
 +
</td>
 +
<td title="lysine" style="width: 2em; background-color: #4747B8;"> Lys
 +
</td>
 +
<td title="methionine" style="width: 2em;background-color: #B8A042;"> Met
 +
</td>
 +
<td title="phenylalanine" style="width: 2em; background-color: #534C52;"> Phe
 +
</td>
 +
<td title="proline" style="width: 2em; background-color: #525252;"> Pro
 +
</td>
 +
<td title="serine" style="width: 2em; background-color: #FF7042;"> Ser
 +
</td>
 +
<td title="threonine" style="width: 2em; background-color: #B84C00;"> Thr
 +
</td>
 +
<td title="tryptophan" style="width: 2em; background-color: #4F4600;"> Trp
 +
</td>
 +
<td title="tyrosine" style="width: 2em; background-color: #8C704C;"> Tyr
 +
</td>
 +
<td title="valine" style="width: 2em; background-color: #FF8CFF;"> Val
 +
</td>
 +
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF00FF;"> Asx
 +
</td>
 +
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF00FF;"> Glx
 +
</td>
 +
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx
 +
</td>
 +
</tr>
 
</table>
 
</table>
  
== Jmol measurements ==
+
===== Nucleotide base residues: Shapely colour scheme =====
* Distance (2 atoms):
+
<table>
# double-click on the starting atom
+
<tr>
# to fix a distance measurement, double-click on second atom</p>
+
<td title="adenine" style="width:2em; background-color: #A0A0FF; text-align: center;"> A
   
+
</td>
* Angle (3 atoms):
+
<td title="guanine" style="width:2em; background-color: #FF7070; text-align: center;"> G
# double-click on the starting atom
+
</td>
# click on the second atom (central atom in angle)
+
<td title="inosine" style="width:2em; background-color: #80FFFF; text-align: center;"> I
# to fix an angle measurement, double-click on third atom</p>
+
</td>
 +
<td title="cytosine" style="width:2em; background-color: #FF8C4B; text-align: center;"> C
 +
</td>
 +
<td title="thymine" style="width:2em; background-color: #A0FFA0; text-align: center;"> T
 +
</td>
 +
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U
 +
</td></tr></table>
 +
 
 +
==== Secondary structure ====
 +
===== Polypeptides, nucleic acids and carbohydrates =====
 +
<table>
 +
<tr>
 +
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix
 +
</td>
 +
<td style="width:5em; background-color: #A00080; text-align: center;">3<sub>10</sub> helix
 +
</td>
 +
<td style="width:5em; background-color: #600080; text-align: center;">π helix
 +
</td>
 +
<td style="width:5em; background-color: #FFC800; text-align: center;">β strand
 +
</td>
 +
<td style="width:5em; background-color: #6080FF; text-align: center;">(β) turn
 +
</td>
 +
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;"> other
 +
</td>
 +
<td style="width:5em; background-color: #FFFFFF; text-align: center;">
 +
</td>
 +
<td style="width:5em; background-color: #AE00FE; text-align: center;">DNA
 +
</td>
 +
<td style="width:5em; background-color: #FD0162; text-align: center;">RNA
 +
</td>
 +
<td style="width:5em; background-color: #FFFFFF; text-align: center; border:1px solid lightgray;">other
 +
</td>
 +
<td style="width:5em; background-color: #FFFFFF; text-align: center;">
 +
</td>
 +
<td style="width:5em; background-color: #A6A6FA; text-align: center;">carbohydrate
 +
</td>
 +
<td style="width:5em; background-color: #808080; text-align: center;">other
 +
</td>
 +
</tr>
 +
</table>
  
* Torsion angle or dihedral (4 atoms)
+
==== Tertiary structure ====
# double-click on the starting atom
+
=====  Polypeptides and nucleic acids =====
# click on the second atom
 
# click on the third atom</p>
 
# to fix a dihedral angle measurement, double-click on fourth atom
 
  
* In all cases:
+
<table style="border-spacing:0;border-collapse:collapse">
** move pointer over destination atom in order to see measurement results without leaving a permanent measurement 
+
<tr>
** move outside the window in order to cancel the measurement
+
<td colspan="16" style="text-align:left">N-terminal or 5’-
** make the same measurement again in order to delete the measurement
+
</td>
 +
<td>
 +
</td>
 +
<td colspan="16" style="text-align:right">C-terminal or 3’-
 +
</td></tr>
 +
<tr style="height:1em">
 +
<td style="width:1em; background-color:#0000ff">
 +
</td>
 +
<td style="width:1em; background-color:#0020ff">
 +
</td>
 +
<td style="width:1em; background-color:#0040ff">
 +
</td>
 +
<td style="width:1em; background-color:#0060ff">
 +
</td>
 +
<td style="width:1em; background-color:#0080ff">
 +
</td>
 +
<td style="width:1em; background-color:#00a0ff">
 +
</td>
 +
<td style="width:1em; background-color:#00c0ff">
 +
</td>
 +
<td style="width:1em; background-color:#00e0ff">
 +
</td>
 +
<td style="width:1em; background-color:#00ffff">
 +
</td>
 +
<td style="width:1em; background-color:#00ffe0">
 +
</td>
 +
<td style="width:1em; background-color:#00ffc0">
 +
</td>
 +
<td style="width:1em; background-color:#00ffa0">
 +
</td>
 +
<td style="width:1em; background-color:#00ff80">
 +
</td>
 +
<td style="width:1em; background-color:#00ff60">
 +
</td>
 +
<td style="width:1em; background-color:#00ff40">
 +
</td>
 +
<td style="width:1em; background-color:#00ff20">
 +
</td>
 +
<td style="width:1em; background-color:#00ff00">
 +
</td>
 +
<td style="width:1em; background-color:#20ff00">
 +
</td>
 +
<td style="width:1em; background-color:#40ff00">
 +
</td>
 +
<td style="width:1em; background-color:#60ff00">
 +
</td>
 +
<td style="width:1em; background-color:#80ff00">
 +
</td>
 +
<td style="width:1em; background-color:#a0ff00">
 +
</td>
 +
<td style="width:1em; background-color:#c0ff00">
 +
</td>
 +
<td style="width:1em; background-color:#e0ff00">
 +
</td>
 +
<td style="width:1em; background-color:#ffff00">
 +
</td>
 +
<td style="width:1em; background-color:#ffe000">
 +
</td>
 +
<td style="width:1em; background-color:#ffc000">
 +
</td>
 +
<td style="width:1em; background-color:#ffa000">
 +
</td>
 +
<td style="width:1em; background-color:#ff8000">
 +
</td>
 +
<td style="width:1em; background-color:#ff6000">
 +
</td>
 +
<td style="width:1em; background-color:#ff4000">
 +
</td>
 +
<td style="width:1em; background-color:#ff2000">
 +
</td>
 +
<td style="width:1em; background-color:#ff0000">
 +
</td></tr></table>
  
 
==More==
 
==More==
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]
+
For further information see:
 +
 
 +
[http://jmol.sourceforge.net Jmol]
 +
 
 +
[http://wiki.jmol.org Jmol Wiki]
 +
 
 +
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]

Latest revision as of 20:59, 30 March 2014

Help with using the Jmol_filter

Jmol mouse control

Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux) and wheel mice.

Action Main (left) button Middle button Secondary (right) button
Jmol menu Click on Jmol logo
or Ctrl + click
  Click
Rotate X,Y Click & drag    
Translate X,Y Shift + double-click & drag Double-click & drag Ctrl + click & drag
Rotate Z Shift + click & drag horizontally Click & drag horizontally Shift + click & drag horizontally
Zoom Shift + click & drag vertically Click & drag vertically
or mouse wheel
 
Reset & centre Shift + double-click (away from molecule) Double-click (away from molecule)  
Resize Jmol Click & drag bottom-right corner    

Jmol measurements

  • Distance between 2 atoms:
  1. double-click on the starting atom
  2. to fix a distance measurement, double-click on second atom
  • Angle between 3 atoms:
  1. double-click on the starting atom
  2. click on the second atom (central atom in angle)
  3. to fix an angle measurement, double-click on third atom
  • Torsion angle or dihedral between 4 atoms:
  1. double-click on the starting atom
  2. click on the second atom
  3. click on the third atom</p>
  4. to fix a dihedral angle measurement, double-click on fourth atom
  • In all cases:
    • move pointer over destination atom in order to see measurement results without leaving a permanent measurement
    • move outside the window in order to cancel the measurement
    • make the same measurement again in order to delete the measurement

Jmol default colours

Elements: CPK colour scheme

Hover over any element to see more information (Atomic Number, Symbol, Element Name)

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18
H He
Li Be B C N O F Ne
Na Mg Al Si P S Cl Ar
K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr
Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe
Cs Ba * Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn
Fr Ra ** Rf Db Sg Bh Hs Mt Ds Rg Cn            
 
  * La Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu  
  ** Ac Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr  

Biological macromolecules

Primary structure

Amino acid residues: Amino colour scheme
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Asx Glx Xxx
Amino acid residues: Shapely colour scheme
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Asx Glx Xxx
Nucleotide base residues: Shapely colour scheme
A G I C T U

Secondary structure

Polypeptides, nucleic acids and carbohydrates
α helix 310 helix π helix β strand (β) turn other DNA RNA other carbohydrate other

Tertiary structure

Polypeptides and nucleic acids
N-terminal or 5’- C-terminal or 3’-

More

For further information see:

Jmol

Jmol Wiki

Jmol Scripting Reference