Colors

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Jmol + JSmol Documentation

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 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
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