Scripting

Jmol + JSmol Documentation

• Description of files in Jmol+JSmol distribution
• File formats read or written by Jmol
• The Jmol scripting interface
  • Scripting as a programming language
  • Complete reference of scripting commands:
    • at St Olaf (primary site)
    • at Jena3D (mirror)
• Loading models directly from databases
• Mouse manual
• Default colors used by Jmol
• Atom sets predefined in Jmol
• Support for bond orders · isotopes · stereochemistry · hydrogen bonds
• Jmol as editor
• Multi-touch support
• Copying and pasting state scripts between applets.
• Backward compatibility (changes of behavior across versions)
• Features added since version 10
• Users mailing list (and a mirror)

The Jmol Application and Applet have a command language that grows on the base of command language of the browser plugin MDL Chime. A set of commands is called a command script, and writing such sets of commands or scripts is called scripting.

Documentation links

Documentation of Jmol's scripting language can be found here:

• http://www.stolaf.edu/academics/chemapps/jmol/

This is the official document. The style is encyclopedic, explaining each command in turn, as usual in reference manuals.

An introduction to Jmol scripting is available here:

• http://www.callutheran.edu/Academic_Programs/Departments/BioDev/omm/scripting/molmast.htm

A more user-friendly, but less thorough, basic guide by Nathan Silva and David Marcey; part of the Online Macromolecular Museum at California Lutheran University.

Similar but different scripting languages

Chime's command language (see "About Chime" at http://molviz.org) is a superset of the command language of Roger Sayle's public domain application RasMol. (The command language of open-source RasMol has diverged somewhat from that in RasMol and Chime). The command language used by Jmol started with most of the Chime commands, but has outgrown it in a notable extent, allowing for many new capabilities.

*-RasMol (v≤2.6)
   |
   |----Chime                Takes nearly all RasMol 2.6 commands and adds a few.
   |     |
   |     ----Jmol (v≥10)     Takes many RasMol 2.6 and Chime 2.6 commands and adds a few.
   |          |
   |          ---Jmol (v≥11) Adds many new commands.
   |
   -----OpenRasMol (v≥2.7)   Takes all RasMol 2.6 commands and adds a few.

Transversal documentation

Covering specific aspects or applications (not by command, and usually not exhaustive):

• Surfaces. Jmol can calculate and render surfaces around a molecule, or part of it, representing its "true" shape and volume. Moreover, isosurfaces, atomic and molecular orbitals, and mathematically defined surfaces can also be rendered.
• Persistent and nonpersistent "set" parameters. Some parameters defined using the "set" command are associated to the app/applet and hence maintained when a new molecule is loaded, while others are reset when the model is removed.

Contributors

AngelHerraez, NicolasVervelle, Marcey, Pimpim