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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.
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.


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|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.
==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%2C_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|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:
The following templates for color keys are currently available:


* Composition (See [[DRuMS]] for how to use Templates).
===Composition===
* Composition color key (See [[DRuMS]] for how to use Templates).
<blockquote><big>
<blockquote><big>
{{Template:ColorKey Composition Protein}}
{{Template:ColorKey Composition Protein}}
Line 14: Line 25:
</big></blockquote>
</big></blockquote>


* Amino to Carboxy Rainbow
===Elements===
See [[DRuMS]] for how to insert the Templates for these color keys.
<blockquote><big>
{{Template:ColorKey_Element_C}}
{{Template:ColorKey_Element_H}}
{{Template:ColorKey_Element_O}}
{{Template:ColorKey_Element_N}}
{{Template:ColorKey_Element_P}}
{{Template:ColorKey_Element_S}}
{{Template:ColorKey_Element_Se}}
</big></blockquote>
 
===Hydrophobic/Polar===
See [[DRuMS]] for how to insert the Templates for these color keys.
<blockquote><big>
{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}
</big></blockquote>
 
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.
<blockquote><big>
{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}
</big></blockquote>
 
===Secondary Structure===
See [[DRuMS]] for how to insert the Templates for these color keys.
<blockquote><big>
{{Template:ColorKey_Helix}},
{{Template:ColorKey_Strand}},
{{Template:ColorKey_Turn}}.
</big></blockquote>
 
===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
<blockquote>
<blockquote>
{{Template:ColorKey_N2CRainbow}}
{{Template:ColorKey_N2CRainbow}}
<br>
{{Template:ColorKey_Amino2CarboxyRainbow}}
</blockquote>
* 5' to 3'  Rainbow for nucleic acid chains
<blockquote>
{{Template:ColorKey_523Rainbow}}
</blockquote>
* Amino to Carboxy Rainbow together with 5' to 3'
<blockquote>
{{Template:ColorKey_N52C3Rainbow}}
</blockquote>
===Temperature Value===
For an explanation, please see [[Temperature color schemes]].
*Fixed (Absolute) Temperature
{{Template:ColorKey_TemperatureFixed}}
*Relative Temperature
{{Template:ColorKey_TemperatureRelative}}
The above keys were generated by including the following Template wikitext blocks:
<pre>
{{Template:ColorKey_TemperatureFixed}}
{{Template:ColorKey_TemperatureRelative}}
</pre>
===ConSurf===
* ConSurf color key (see [[Evolutionary Conservation]]). This 11-color key covers all cases.
<blockquote>
{{Template:ColorKey_ConSurf}}
</blockquote>
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:
<blockquote>
{{Template:ColorKey_ConSurf_NoYellow}}
</blockquote>
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:
<blockquote>
{{Template:ColorKey_ConSurf_NoGray}}
</blockquote>
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:
<blockquote>
{{Template:ColorKey_ConSurf_NoYellow_NoGray}}
</blockquote>
</blockquote>


The above keys were generated by including the following Template wikitext blocks:
<pre>
{{Template:ColorKey_ConSurf}}
{{Template:ColorKey_ConSurf_NoYellow}}
{{Template:ColorKey_ConSurf_NoGray}}
{{Template:ColorKey_ConSurf_NoYellow_NoGray}}
</pre>
===Other Color Schemes?===
If you would like help setting up a Template in Proteopedia for a color key not yet available, please contact {{Template:Contact}}.
If you would like help setting up a Template in Proteopedia for a color key not yet available, please contact {{Template: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
<center><big><b><font color='red'>Red</font> and <font color='green'>Green</font></b></big></center>
enter the following in the wikitext box:
<br><nowiki>
<center><big><b><font color='red'>Red</font> and <font color='green'>Green</font></b></big></center>
</nowiki>
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 [http://jmol.sourceforge.net/jscolors/index.en.html Jmol Colors] page. For example,
<center><big><b><font color='#cc80ff'>Lithium</font> and <font color='#c88033'>Copper</font></b></big></center>
can be produced with
<br><nowiki>
<center><big><b><font color='#cc80ff'>Lithium</font> and <font color='#c88033'>Copper</font></b></big></center>
</nowiki>
==See Also==
* [[DRuMS]] including how to use color key templates.
* [[Help:Editing]]

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Eric Martz
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