Difference between revisions of "Jmol Help"

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     </tr>
 
     </tr>
 
</table>
 
</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 ==
 
== Jmol default colours ==
=== Elements ===
+
=== 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="width: 1em; 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="width: 1em; 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="width: 1em; background-color:#cc80ff">Li</td>
+
       <td title="3 Li Lithium" style="background-color:#cc80ff">Li</td>
       <td title="4 Be Beryllium" style="width: 1em; background-color:#c2ff00">Be</td>
+
       <td title="4 Be Beryllium" style="background-color:#c2ff00">Be</td>
 
       <td colspan="10"></td>
 
       <td colspan="10"></td>
 
       <td title="5 B Boron" bgcolor="#ffb5b5">B</td>
 
       <td title="5 B Boron" bgcolor="#ffb5b5">B</td>
Line 155: 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 212: Line 253:
 
=== Biological macromolecules ===
 
=== Biological macromolecules ===
 
==== Primary structure ====
 
==== Primary structure ====
===== Amino acid residues =====
+
===== Amino acid residues: Amino colour scheme =====
 +
<table style="text-align: center;">
 +
<tr>
 +
<td title="alanine" style="width: 2em; background-color: #C8C8C8"> Ala
 +
</td>
 +
<td title="arginine" style="width: 2em; background-color: #145AFF"> Arg
 +
</td>
 +
<td title="asparagine" style="width: 2em; background-color: #00DCDC"> Asn
 +
</td>
 +
<td title="aspartic acid" style="width: 2em; background-color: #E60A0A"> Asp
 +
</td>
 +
<td title="cystine" style="width: 2em; background-color: #E6E600"> Cys
 +
</td>
 +
<td title="glutamine" style="width: 2em; background-color: #00DCDC"> Gln
 +
</td>
 +
<td title="glutamic acid" style="width: 2em; background-color: #E60A0A"> Glu
 +
</td>
 +
<td title="glycine" style="width: 2em; background-color: #EBEBEB; border:1px solid lightgray;"> Gly
 +
</td>
 +
<td title="histidine" style="width: 2em; background-color: #8282D2"> His
 +
</td>
 +
<td title="isoleucine" style="width: 2em; background-color: #0F820F"> Ile
 +
</td>
 +
<td title="leucine" style="width: 2em; background-color: #0F820F"> Leu
 +
</td>
 +
<td title="lysine" style="width: 2em; background-color: #145AFF"> Lys
 +
</td>
 +
<td title="methionine" style="width: 2em;background-color: #E6E600"> Met
 +
</td>
 +
<td title="phenylalanine" style="width: 2em; background-color: #3232AA"> Phe
 +
</td>
 +
<td title="proline" style="width: 2em; background-color: #DC9682"> Pro
 +
</td>
 +
<td title="serine" style="width: 2em; background-color: #FA9600"> Ser
 +
</td>
 +
<td title="threonine" style="width: 2em; background-color: #FA9600"> Thr
 +
</td>
 +
<td title="tryptophan" style="width: 2em; background-color: #B45AB4"> Trp
 +
</td>
 +
<td title="tyrosine" style="width: 2em; background-color: #3232AA"> Tyr
 +
</td>
 +
<td title="valine" style="width: 2em; background-color: #0F820F"> Val
 +
</td>
 +
<td title="aspartate or asparagine" style="width: 2em; background-color: #FF69B4"> Asx
 +
</td>
 +
<td title="glutamic acid or glutamine" style="width: 2em; background-color: #FF69B4"> Glx
 +
</td>
 +
<td title="other" style="width: 2em; background-color: #BEA06E"> Xxx
 +
</td>
 +
</tr>
 +
</table>
 +
===== Amino acid residues: Shapely colour scheme =====
 
<table style="text-align: center;">
 
<table style="text-align: center;">
 
<tr>
 
<tr>
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala
+
<tr>
 +
<td title="alanine" style="width: 2em; background-color: #8CFF8C"> Ala
 
</td>
 
</td>
 
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg
 
<td title="arginine" style="width: 2em; background-color: #00007C;"> Arg
Line 223: Line 316:
 
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp
 
<td title="aspartic acid" style="width: 2em; background-color: #A00042"> Asp
 
</td>
 
</td>
<td title="cystine" style="width: 2em; background-color: #A00042;"> Cys
+
<td title="cystine" style="width: 2em; background-color: #FFFF70;"> Cys
 
</td>
 
</td>
 
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln
 
<td title="glutamine" style="width: 2em; background-color: #006BFF;"> Gln
Line 260: Line 353:
 
</td>
 
</td>
 
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx
 
<td title="other" style="width: 2em; background-color: #FF00FF;"> Xxx
</td></tr></table>
+
</td>
<h5> <span class="mw-headline" id="Nucleotide_base_residues"> Nucleotide base residues </span></h5>
+
</tr>
 +
</table>
 +
 
 +
===== Nucleotide base residues: Shapely colour scheme =====
 
<table>
 
<table>
 
<tr>
 
<tr>
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<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U
 
<td title="uracil" style="width:2em; background-color: #FF8080; text-align: center;"> U
 
</td></tr></table>
 
</td></tr></table>
 +
 
==== Secondary structure ====
 
==== Secondary structure ====
 
+
===== Polypeptides, nucleic acids and carbohydrates =====
 
<table>
 
<table>
<tr>
 
<td colspan="6">Polypeptides</td>
 
<td></td>
 
<td colspan="3">Nucleic acids</td>
 
</tr>
 
 
<tr>
 
<tr>
 
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix
 
<td style="width:5em; background-color: #FF0080; text-align: center;">α helix
Line 392: Line 484:
 
<td style="width:1em; background-color:#ff0000">
 
<td style="width:1em; background-color:#ff0000">
 
</td></tr></table>
 
</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</p>
 
   
 
* 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</p>
 
 
* 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
 
  
 
==More==
 
==More==

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