Technical Support - Jmol

Jmol is an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules. Jmol provides its own menu that enables users to toggle between different molecular display options. Right click the mouse to open the menu. Some of the menu options are listed below. For more information on Jmol, see http://jmol.sourceforge.net. A detailed explanation of Jmol commands can be found here.

1. Save: this option can be used to save molecules from the Jmol window. Select JPG Image to save a molecule as a picture. Select Script with state to save the molecule as a three-dimensional model that can be viewed in Jmol.
   
   
2. Model: this option is active when the file contains more than one molecular model. Use this option to toggle between models or display them together.
   
   
3. Select: use this option to select all atoms or a specific atom. Select an atom or atoms to change the color, to display labels, or to execute other options with respect to part of the molecule.
   
   
4. Style: opens a sub-menu containing the following items:
   
   
   1. Scheme - several display formats are available. Among them are:
      • Ball & Stick - sticks represent chemical bonds and balls represent atoms
      • Wireframe - lines represent chemical bonds and vertices represent atoms
      • Sticks - sticks represent chemical bonds and vertices represent atoms
      
      
   2. Atoms - choose show hydrogens to show or hide hydrogen atoms. Click off to hide all atoms. Control the size of balls in all atoms, using the van der Waals 15%-100% option.
      
      
   3. Labels - select the appropriate option to display atom symbols and serial numbers.
      
      
   4. Bonds - choose on or off to show or hide chemical bonds. Select the thickness of bonds from 0.10Å to 0.30Å.


5. Color: this menu controls the color scheme of atoms, bonds and other items on the screen. The default color scheme is the CPK. This scheme was developed by Corey and Pauling and later enhanced by Koltun (hence the name CPK), and initially used to mark atoms in plastic models. Atom colors are specified on the Jmol website help site.
   
   
6. Zoom: changes the molecule size on the Jmol screen. Size can also be changed using the mouse wheel.
   
   
7. Spin: rotates molecule automatically around the Z-axis. Click On to start and Off to stop.
   
   
8. Measurement: use this sub-menu to display bond lengths, bond angles and torsion angles. To display bond length, choose click for distance measurement. Then click on two atoms on the screen. Note that the chosen atoms are displayed on the status bar of the html page. The bond length will appear on the screen. Click on the same two atoms to delete the bond length. To display bond angle, choose click for angle measurement. Then click on three atoms on the screen. To display torsion angles, choose click for torsion (dihedral) measurement. Then click on four atoms on the screen. Choose delete measurements to remove all measurements from the screen.
   
   
9. Console: this option opens another window that is divided into two parts. At the bottom, users can write Jmol commands. The results and error messages (if any) are displayed at the top, and in the Jmol window. A full list of Jmol commands can be found here.