Note: You are currently viewing documentation for Moodle 3.2. Up-to-date documentation for the latest stable version of Moodle is probably available here: Jmol Help.

Jmol Help: Difference between revisions

From MoodleDocs
Line 210: Line 210:


== Jmol measurements ==
== Jmol measurements ==
<ul>
* Distance (2 atoms):
  <li>
     # double-click on the starting atom
    <p> Distance (2 atoms):</p>
    # to fix a distance measurement, double-click on second atom</p>
     <ol>
   
      <li>
* Angle (3 atoms):
        <p>double-click on the starting atom</p>
     # double-click on the starting atom
      </li>
    # click on the second atom (central atom in angle)
      <li>
    # to fix an angle measurement, double-click on third atom</p>
        <p>to fix a distance measurement, double-click on second atom</p>
 
      </li>
* Torsion angle or dihedral (4 atoms)
    </ol>
     # double-click on the starting atom
  </li>
    # click on the second atom
  <li>
    # click on the third atom</p>
    <p> Angle (3 atoms):</p>
    # to fix a dihedral angle measurement, double-click on fourth atom
     <ol>
* In all cases:
      <li>
     * move pointer over destination atom in order to see measurement results without leaving a permanent measurement  
        <p>double-click on the starting atom</p>
    * move outside the window in order to cancel the measurement
      </li>
    * make the same measurement again in order to delete the measurement
      <li>
        <p>click on the second atom (central atom in angle) </p>
      </li>
      <li>
        <p>to fix an angle measurement, double-click on third atom</p>
      </li>
    </ol>
  </li>
  <li>
    <p> Torsion angle or dihedral (4 atoms)</p>
     <ol>
      <li>
        <p>double-click on the starting atom</p>
      </li>
      <li>
        <p>click on the second atom</p>
      </li>
      <li>
        <p>click on the third atom</p>
      </li>
      <li>
        <p>to fix a dihedral angle measurement, double-click on fourth atom</p>
      </li>
    </ol>
  </li>
  <li>
    <p> In all cases:</p>
     <ul>
      <li>
        <p> move pointer over destination atom in order to see measurement results without leaving a permanent measurement</p>
      </li>
      <li>
        <p> move outside the window in order to cancel the measurement</p>
      </li>
      <li>
        <p> make the same measurement again in order to delete the measurement</p>
      </li>
    </ul>
  </li>
</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 15:01, 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):
   # double-click on the starting atom

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

  • Angle (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 (4 atoms)
   # double-click on the starting atom
   # click on the second atom

# click on the third atom

   # 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]

Retrieved from "https://docs.moodle.org/32/en/index.php?title=Jmol_Help&oldid=111477"
Powered by MediaWiki