Difference between revisions of "Colors"
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Jmol + JSmol Documentation
AngelHerraez (talk | contribs) (demo isotopes color: add natural isotopes) |
AngelHerraez (talk | contribs) (proposal for color change in N and C isotopes) |
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{| | {| | ||
|- | |- | ||
| − | ! isotope !! color !! color code !! script syntax | + | ! isotope !! color !! color code !! script syntax !! proposed color |
|- | |- | ||
|'''<sup>1</sup>H''' | |'''<sup>1</sup>H''' | ||
| Line 36: | Line 36: | ||
|<sup>11</sup>C | |<sup>11</sup>C | ||
||<div style="background-color:#D8D8D8;width:50px;"> </div> | ||<div style="background-color:#D8D8D8;width:50px;"> </div> | ||
| − | || [xD8D8D8] || _11C | + | || [xD8D8D8] || _11C |
| + | ||<div style="background-color:#C0C0C0;width:50px;">new</div> | ||
|- | |- | ||
|'''<sup>12</sup>C''' | |'''<sup>12</sup>C''' | ||
||<div style="background-color:#909090;width:50px;"> </div> | ||<div style="background-color:#909090;width:50px;"> </div> | ||
|| [x909090] || _12C | || [x909090] || _12C | ||
| + | ||<div style="background-color:#909090;width:50px;">same</div> | ||
|- | |- | ||
|<sup>13</sup>C | |<sup>13</sup>C | ||
||<div style="background-color:#505050;width:50px;"> </div> | ||<div style="background-color:#505050;width:50px;"> </div> | ||
|| [x505050] || _13C | || [x505050] || _13C | ||
| + | ||<div style="background-color:#686868;width:50px;">new</div> | ||
|- | |- | ||
|<sup>14</sup>C | |<sup>14</sup>C | ||
||<div style="background-color:#404040;width:50px;"> </div> | ||<div style="background-color:#404040;width:50px;"> </div> | ||
|| [x404040] || _14C | || [x404040] || _14C | ||
| + | ||<div style="background-color:#404040;width:50px;">same</div> | ||
|- | |- | ||
|'''<sup>14</sup>N''' | |'''<sup>14</sup>N''' | ||
||<div style="background-color:#3050F8;width:50px;"> </div> | ||<div style="background-color:#3050F8;width:50px;"> </div> | ||
|| [x3050F8] || _14N | || [x3050F8] || _14N | ||
| + | ||<div style="background-color:#3050F8;width:50px;">same</div> | ||
|- | |- | ||
|<sup>15</sup>N | |<sup>15</sup>N | ||
||<div style="background-color:#105050;width:50px;"> </div> | ||<div style="background-color:#105050;width:50px;"> </div> | ||
|| [x105050] || _15N | || [x105050] || _15N | ||
| + | ||<div style="background-color:#2137AA;width:50px;">new</div> | ||
|} | |} | ||
Revision as of 18:39, 18 April 2009
- 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 | 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
|
