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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">
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       <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>
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=== Biological macromolecules ===
=== Biological macromolecules ===
==== Primary structure ====
==== Primary structure ====
===== Amino acid residues =====
===== Amino acid residues: Amino colour scheme =====
<table style="text-align: center;">
<table style="text-align: center;">
<tr>
<tr>
<td title="alanine" style="width: 2em; background-color: #8CFF8C;"> Ala
<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;">
<tr>
<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
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<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
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</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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==== Secondary structure ====
==== Secondary structure ====
===== Polypeptides, nucleic acids and carbohydrates
===== Polypeptides, nucleic acids and carbohydrates =====
<table>
<table>
<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
</td>
</td>
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<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

  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