Scripting
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.
- 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.
