Scripting

Jmol / JSmol Tutorials

• A list of Jmol / JSmol Tutorials written by users.
• Using the mouse (English · Español · Français · Japanese).
• Scripting quickstart: rendering options · selecting atoms.
• How to create surfaces and isosurfaces, including cavities, pockets and tunnels.
• Displaying shapes, polyhedra, orbitals, dipoles, distances, forces and vibrations.
• Creating movies.
• Customizing Jmol: macros · menus.
• Web pages without writing code by using the Jmol "Export to Web" function.

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