Colors

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)

Default colors used by Jmol

Several users have asked about a guide to colors used by Jmol by default.

This documentation is now available on Jmol website here. Suggestions are welcome for future improvements, via jmol-users mailing list.

The plan is:

• colors for atoms (by element) --done
• colors for chains --done
• colors for groups / residues --done
• alternative color patterns: Jmol, Rasmol, DRuMS --partly done
• anything else?

Support for isotopes

Common isotopes are recognized by Jmol and colored slightly lighter or darker than the element color:

²H = D = deuterium = [xFFFFC0]

³H = T = tritium = [xFFFFA0]

¹¹C = [xD8D8D8] (added on 29 Nov. 2007)

¹³C = [x505050]

¹⁴C = [x404040]

¹⁵N = [x105050]

Contributors

AngelHerraez, NicolasVervelle, Pimpim