Scripting

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Jmol + JSmol Documentation

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:

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:

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. An introductory tutorial on creating macromolecular Jmol surfaces is available: An Introduction to Jmol Surface Displays, part of the Online Macromolecular Museum at California Lutheran University.
  • 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.