Colors
- 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:
- 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:
| isotope | color | color code | script syntax |
|---|---|---|---|
| 2H | [xFFFFC0] | _2H, _D, deuterium | |
| 3H | [xFFFFA0] | _3H, _T, tritium | |
| 11C | [xD8D8D8] | _11C | |
| 13C | [x505050] | _13C | |
| 14C | [x404040] | _14C | |
| 15N | [x105050] | _15N |
