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:

.........(color code)......(script syntax)

²H => [xFFFFC0] => _2H, D, deuterium

³H => [xFFFFA0] => _3H, T, tritium

¹¹C => [xD8D8D8] => _11C (added on 29 Nov. 2007)

¹³C => [x505050] => _13C

¹⁴C => [x404040] => _14C

¹⁵N => [x105050] => _15N

Contributors

AngelHerraez, NicolasVervelle, Pimpim