Difference between revisions of "Jmol Help"

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(Amino acid residues)
(Amino acid residues)
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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
Line 332: Line 332:
 
</tr>
 
</tr>
 
</table>
 
</table>
 +
 
===== Nucleotide_base_residues =====
 
===== Nucleotide_base_residues =====
 
<table>
 
<table>

Revision as of 20:11, 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 default colours

Elements

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                  
 
  * 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
Ala Arg Asn Asp Cys Gln Glu Gly His Ile Leu Lys Met Phe Pro Ser Thr Trp Tyr Val Asx Glx Xxx
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
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’-

Jmol measurements

  • Distance between 2 atoms:
  1. double-click on the starting atom
  2. to fix a distance measurement, double-click on second atom</p>
  • 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</p>
  • 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

More

For further information see:

Jmol

Jmol Wiki

Jmol Scripting Reference