Difference between revisions of "Jmol Help"

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For further information see:  
For further information see:
[http://jmol.sourceforge.net Jmol]
[http://jmol.sourceforge.net Jmol]
[http://wiki.jmol.org Jmol Wiki]
[http://wiki.jmol.org Jmol Wiki]
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]
[http://chemapps.stolaf.edu/jmol/docs Jmol Scripting Reference]

Revision as of 15:34, 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
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 element colours

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

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  

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


For further information see: Jmol Jmol Wiki Jmol Scripting Reference