Difference between revisions of "Colors"

Revision as of 15:57, 6 April 2009

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)

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:

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

isotope	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

@@ Line 18: / Line 18: @@
 Common isotopes are recognized by Jmol and colored slightly lighter or darker than the element color:
-:.........(color code)......(script syntax)
+{|
-:<sup>2</sup>H => [xFFFFC0]  =>  _2H, D, deuterium
+|-
-:<sup>3</sup>H => [xFFFFA0]  =>  _3H, T, tritium
+! isotope !! color !! color code !! script syntax
-:<sup>11</sup>C => [xD8D8D8] =>  _11C   (added on 29 Nov. 2007)
+|-
-:<sup>13</sup>C => [x505050] =>  _13C
+|<sup>2</sup>H
-:<sup>14</sup>C => [x404040] =>  _14C
+||<div style="background-color:#FFFFC0;width:50px;">&nbsp;</div>
-:<sup>15</sup>N => [x105050] =>  _15N
+|| [xFFFFC0] || _2H, _D, deuterium
+|-
+|<sup>3</sup>H
+||<div style="background-color:#FFFFA0;width:50px;">&nbsp;</div>
+|| [xFFFFA0] || _3H, _T, tritium
+|-
+|<sup>11</sup>C
+||<div style="background-color:#D8D8D8;width:50px;">&nbsp;</div>
+|| [xD8D8D8] || _11C
+|-
+|<sup>13</sup>C
+||<div style="background-color:#505050;width:50px;">&nbsp;</div>
+|| [x505050] || _13C
+|-
+|<sup>14</sup>C
+||<div style="background-color:#404040;width:50px;">&nbsp;</div>
+|| [x404040] || _14C
+|-
+|<sup>15</sup>N
+||<div style="background-color:#105050;width:50px;">&nbsp;</div>
+|| [x105050] || _15N
+|}