Help:Color Keys
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Color Keys
A molecular scene usually communicates best when a color key is provided. It is planned that a future version of Proteopedia will provide a mechanism to place a color key in the legend or caption beneath the molecular scene in Jmol (see Proteopedia:Wishlist), but this is not yet available. At present, you can put colored text or an image in the wikitext of your page.
Examples
- Many color keys are used in the article on the Lac repressor.
- The amino to carboxy color key is used in NMR_Ensembles_of_Models#Display_of_NMR_Models_by_Proteopedia.
- The ConSurf color key is used in Avian_Influenza_Neuraminidase,_Tamiflu_and_Relenza#Influenza_Virus_Neuraminidase
Color Key Templates
Templates are available to make it easy to insert a color key for some of the standard color schemes that are available on buttons under the Colors tab in the Scene Authoring Tool. How to insert a color key template into wikitext is is explained on the page about the DRuMS Standard Color Schemes, where you will also see examples of color keys as colored wikitext. Also, you can view the source of this page to see how it is done.
The following templates for color keys are currently available:
Composition
- Composition color key (See DRuMS for how to use Templates).
Protein DNA RNA Ligand Solvent
Elements
See DRuMS for how to insert the Templates for these color keys.
C H O N P S Se
Hydrophobic/Polar
See DRuMS for how to insert the Templates for these color keys.
Hydrophobic, Polar
In Proteopedia's SAT is a button hydrophobic/polar. It applies these two colors according to the definitions built into Jmol:
- Hydrophobic: Ala, Cys, Gly, Ile, Leu, Met, Phe, Pro, Trp, Tyr, Val.
- Polar: Arg, Asn, Asp, Gln, Glu, His, Lys, Ser, Thr.
Jmol's categories attempt to categorize the sidechains as to their predominant characteristic. This is an oversimplification as Trp and Tyr have polar atoms; Arg, Gln, Glu, Lys have several aliphatic carbons, and His has an aromatic ring.
Charge
See DRuMS for how to insert the Templates for these color keys.
Anionic (-) / Cationic (+)
Secondary Structure
See DRuMS for how to insert the Templates for these color keys.
Alpha Helices, Beta Strands , Turns.
Rainbows: N to C, 5' to 3'
See DRuMS for how to insert the Templates for these color keys.
- Amino to Carboxy Rainbow (N->C Rainbow) color key for protein chains
N C
Amino Terminus Carboxy Terminus
- 5' to 3' Rainbow for nucleic acid chains
5' 3'
- Amino to Carboxy Rainbow together with 5' to 3'
N, 5' C, 3'
Temperature Value
For an explanation, please see Temperature color schemes.
- Fixed (Absolute) Temperature
| 0 | 50 | 100 |
- Relative Temperature
| min temp | max temp |
The above keys were generated by including the following Template wikitext blocks:
{{Template:ColorKey_TemperatureFixed}}
{{Template:ColorKey_TemperatureRelative}}
ConSurf
- ConSurf color key (see Evolutionary Conservation). This 11-color key covers all cases.
Only when your ConSurf-colored model has no yellow residues (residues with insufficient data in the multiple sequence alignment) it is OK to use this 10-color key:
Only when your ConSurf-colored model has no gray residues ("no data" chains that ConSurf could not process) it is OK to use this 10-color key:
Only when your ConSurf-colored model has no yellow residues (residues with insufficient data in the multiple sequence alignment), and has no gray residues ("no data" chains that ConSurf could not process), it is OK to use this 9-color key:
The above keys were generated by including the following Template wikitext blocks:
{{Template:ColorKey_ConSurf}}
{{Template:ColorKey_ConSurf_NoYellow}}
{{Template:ColorKey_ConSurf_NoGray}}
{{Template:ColorKey_ConSurf_NoYellow_NoGray}}
Other Color Schemes?
If you would like help setting up a Template in Proteopedia for a color key not yet available, please contact 
.
Coloring Text
If one of the templates above does not provide what you need, you can color text using HTML. For example, to produce
enter the following in the wikitext box:
<center><big><b><font color='red'>Red</font> and <font color='green'>Green</font></b></big></center>
The above example uses color names red and green. For more exotic colors, you can use Red-Green-Blue hexadecimal codes instead of color names. An extensive list of such codes is on the Jmol Colors page. For example,
can be produced with
<center><big><b><font color='#cc80ff'>Lithium</font> and <font color='#c88033'>Copper</font></b></big></center>
See Also
- DRuMS including how to use color key templates.
- Help:Editing
