Help:Color Keys: Difference between revisions
Eric Martz (talk | contribs) →Color Key Templates: polishing |
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==Examples== | ==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 amino to carboxy color key is used in [[NMR_Ensembles_of_Models#Display_of_NMR_Models_by_Proteopedia]]. | ||
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===Elements=== | ===Elements=== | ||
See [[DRuMS]] for how to insert the Templates for these color keys. | |||
<blockquote><big> | <blockquote><big> | ||
{{Template:ColorKey_Element_C}} | {{Template:ColorKey_Element_C}} | ||
| Line 29: | Line 32: | ||
{{Template:ColorKey_Element_O}} | {{Template:ColorKey_Element_O}} | ||
{{Template:ColorKey_Element_N}} | {{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> | </big></blockquote> | ||
===Secondary Structure=== | ===Secondary Structure=== | ||
See [[DRuMS]] for how to insert the Templates for these color keys. | |||
<blockquote><big> | <blockquote><big> | ||
{{Template:ColorKey_Helix}}, | {{Template:ColorKey_Helix}}, | ||
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===Rainbows: N to C, 5' to 3'=== | ===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 | * Amino to Carboxy Rainbow (N->C Rainbow) color key for protein chains | ||
<blockquote> | <blockquote> | ||
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{{Template:ColorKey_N52C3Rainbow}} | {{Template:ColorKey_N52C3Rainbow}} | ||
</blockquote> | </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=== | ||
* ConSurf color key (see [[Evolutionary Conservation]]) | * ConSurf color key (see [[Evolutionary Conservation]]). This 11-color key covers all cases. | ||
<blockquote> | <blockquote> | ||
{{Template:ColorKey_ConSurf}} | {{Template:ColorKey_ConSurf}} | ||
</blockquote> | </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> | |||
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?=== | ===Other Color Schemes?=== | ||