Difference between revisions of "Jmol Help"

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(Jmol mouse control)
(Jmol measurements)
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   <li>
 
   <li>
 
     <p> Distance (2 atoms):</p>
 
     <p> Distance (2 atoms):</p>
     <ol type="1">
+
     <ol>
 
       <li>
 
       <li>
 
         <p>double-click on the starting atom</p>
 
         <p>double-click on the starting atom</p>
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   <li>
 
   <li>
 
     <p> Angle (3 atoms):</p>
 
     <p> Angle (3 atoms):</p>
     <ol type="1">
+
     <ol>
 
       <li>
 
       <li>
 
         <p>double-click on the starting atom</p>
 
         <p>double-click on the starting atom</p>
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   <li>
 
   <li>
 
     <p> Torsion angle or dihedral (4 atoms)</p>
 
     <p> Torsion angle or dihedral (4 atoms)</p>
     <ol type="1">
+
     <ol>
 
       <li>
 
       <li>
 
         <p>double-click on the starting atom</p>
 
         <p>double-click on the starting atom</p>
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   </li>
 
   </li>
 
</ul>
 
</ul>
 +
 
==More==
 
==More==
 
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]
 
For further information see: [[http://jmol.sourceforge.net http://jmol.sourceforge.net]]

Revision as of 14:55, 30 March 2014

Help with using the Jmol_filter

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 mouse control

Jmol controls for 1-button (e.g. Macintosh), 2-button (e.g. Windows), 3-button (e.g. Linux), or 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 (2 atoms):

    1. double-click on the starting atom

    2. to fix a distance measurement, double-click on second atom

  • Angle (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 (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

More

For further information see: [http://jmol.sourceforge.net]