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

Documentation on colors in Jmol.

Support for isotopes

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

isotope	color	color code	script syntax	proposed color
1H		[xFFFFFF]	_1H
2H		[xFFFFC0]	_2H, _D, deuterium
3H		[xFFFFA0]	_3H, _T, tritium
11C		[xD8D8D8]	_11C	new
12C		[x909090]	_12C	same
13C		[x505050]	_13C	new
14C		[x404040]	_14C	same
14N		[x3050F8]	_14N	same
15N		[x105050]	_15N	new

Contributors

AngelHerraez, NicolasVervelle, Pimpim