Scripting

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Jmol + JSmol Documentation

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The Jmol Application and Applet have a command language that grew on the base of the command language of RasMol and its browser plugin MDL Chime. A set of commands is called a command script, and writing such sets of commands or scripts is called scripting. This is the major way of controlling the display of molecules in Jmol.

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. In addition to this primary site, with latest updates, there are some mirror sites (see links at right).

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.

Other

  • Scripts can be included inside the molecular model file. See how to do it.
  • Jmol scripting language has grown, among other features, by adding mathematical operators (JmolMath), control structures (loops, conditionals, etc.). You may be interested in this programming language approach.

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.

RasMol commands not accepted by Jmol

These are some RasMol / OpenRasMol commands that are not accepted by Jmol (they will raise an error and will stop further execution of the script):

  • set cartoon on defines that cartoon display should use arrowheads -- not needed in Jmol, since that is the default (and not changeable).
  • set cartoon N defines the "depth" (i.e. thickness) of the ribbons; more or less similar to Jmol's cartoon N.
  • color atom cpknew "cpkNew" is a color scheme for elements slightly diferent than the old default "cpk"; not available as such in Jmol. See Jmol Colors for a comparison.

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.
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