DRuMS: Difference between revisions
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==What is DRuMS?== | ==What is DRuMS?== | ||
DRuMS refers to a set of standard color schemes for macromolecular visualization, released in 2000. The official DRuMS website is [http://www.umass.edu/molvis/drums/ www.umass.edu/molvis/drums]. DRuMS color schemes are derived in part from those used in the popular molecular visualization programs RasMol, and are used in Chime, [http://proteinexplorer.org Protein Explorer], the [http://bioinformatics.org/jmol-tutorials Jmol Tutorial-Authoring Template], and [http://www.worthpublishers.com/lehninger3d Biochemistry in 3D], the latter being a set of online 3D structure tutorials that accompanied ''Lehninger Principles of Biochemistry, 3rd Ed.''. The name ''DRuMS'' represents the names of its authors: [http://www.molvisions.com Timothy '''D'''riscoll], [http://moleculesinmotion.com Frieda '''R'''eichsman], [http://martz.molviz.org Eric '''M'''artz], and Roger A. '''S'''ayle (author of RasMol). | DRuMS refers to a set of standard color schemes for macromolecular visualization, released in 2000. The official DRuMS website is [http://www.umass.edu/molvis/drums/ www.umass.edu/molvis/drums]. DRuMS color schemes are derived in part from those used in the popular molecular visualization programs [[RasMol]], and are used in [[Proteopedia]], [[Jmol]] (see [http://jmol.sourceforge.net/jscolors/ Jmol Colors]), [[Chime]], [http://proteinexplorer.org Protein Explorer], the [http://bioinformatics.org/jmol-tutorials Jmol Tutorial-Authoring Template], and [http://www.worthpublishers.com/lehninger3d Biochemistry in 3D], the latter being a set of online 3D structure tutorials that accompanied ''Lehninger Principles of Biochemistry, 3rd Ed.''. The name ''DRuMS'' represents the names of its authors: [http://www.molvisions.com Timothy '''D'''riscoll], [http://moleculesinmotion.com Frieda '''R'''eichsman], [http://martz.molviz.org Eric '''M'''artz], and Roger A. '''S'''ayle (author of RasMol). | ||
==The DRuMS Color Schemes== | ==The DRuMS Color Schemes== | ||
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{{Template:ColorKey Composition Protein}}, {{Template:ColorKey Composition DNA}}, {{Template:ColorKey Composition Ligand}}. | {{Template:ColorKey Composition Protein}}, {{Template:ColorKey Composition DNA}}, {{Template:ColorKey Composition Ligand}}. | ||
If you enclose the wiki text in <nowiki>< | If you enclose the wiki text in <nowiki><span style="font-size:150%">...</span></nowiki> tags, it will look like this: | ||
< | <span style="font-size:150%">{{Template:ColorKey Composition Protein}}, {{Template:ColorKey Composition DNA}}, {{Template:ColorKey Composition Ligand}}.</span> | ||
===Composition=== | ===Composition=== | ||
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{{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}} | |||
{{Template:ColorKey_Element_Fe}} | |||
The above colored element symbols were generated by including the following Template wikitext blocks: | The above colored element symbols were generated by including the following Template wikitext blocks: | ||
| Line 58: | Line 62: | ||
{{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}} | |||
{{Template:ColorKey_Element_Fe}} | |||
</pre> | </pre> | ||
If you need additional elements, simply create the appropriate Template page, using [http://jmol.sourceforge.net/jscolors/ Jmol Colors], or contact {{Template:Martz_email}}. Be sure to include additional elements in the lists above. | |||
===Hydrophobic/Polar=== | ===Hydrophobic/Polar=== | ||
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<blockquote><big> | <blockquote><big> | ||
{{Template:ColorKey_Helix}}, | {{Template:ColorKey_Helix}}, | ||
{{Template:ColorKey_310Helix}}, | |||
{{Template:ColorKey_PiHelix}}, | |||
{{Template:ColorKey_Strand}}, | {{Template:ColorKey_Strand}}, | ||
{{Template:ColorKey_Loop}}, | |||
{{Template:ColorKey_Turn}}. | {{Template:ColorKey_Turn}}. | ||
</big></blockquote> | </big></blockquote> | ||
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<pre> | <pre> | ||
{{Template:ColorKey_Helix}}, | {{Template:ColorKey_Helix}}, | ||
{{Template:ColorKey_310Helix}}, | |||
{{Template:ColorKey_PiHelix}}, | |||
{{Template:ColorKey_Strand}}, | {{Template:ColorKey_Strand}}, | ||
{{Template:ColorKey_Loop}}, | |||
{{Template:ColorKey_Turn}}. | {{Template:ColorKey_Turn}}. | ||
</pre> | </pre> | ||
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{{Template:ColorKey_N52C3Rainbow}} | {{Template:ColorKey_N52C3Rainbow}} | ||
</pre> | </pre> | ||
===Additional DRuMS ColorKey Templates=== | |||
Proteopedia's ''Scene Authoring Tool'' implement much of the DRuMS color schemes, but not all. | |||
Several portions not implemented concern nucleotides. These are based on the following mnemonics for A, C, G, T, & U: | |||
<br><b><big> | |||
<font color="#5050ff">Azure</font>, | |||
<font color="#e00000">Crimson</font>, | |||
<font color="#00c000">Green</font>, | |||
<font color="#d0d000">Tweety Bird</font>, | |||
<font color="#cc9900">Umber</font>.</big></b> | |||
<blockquote><big> | |||
{{Template:ColorKey Purines}}, {{Template:ColorKey Pyrimidines}}, | |||
<br> | |||
{{Template:ColorKey Bases Nucleotides}}, | |||
<br> | |||
{{Template:ColorKey Bases DNA}}, | |||
<br> | |||
{{Template:ColorKey Bases RNA}}. | |||
</big></blockquote> | |||
The above colored terms were generated by including the following Template wikitext blocks: | |||
<pre> | |||
{{Template:ColorKey Purines}} | |||
{{Template:ColorKey Pyrimidines}} | |||
{{Template:ColorKey Bases Nucleotides}} | |||
{{Template:ColorKey Bases DNA}} | |||
{{Template:ColorKey Bases RNA}} | |||
</pre> | |||
<applet load='Image:Kt7.pdb.gz' size='150' frame='true' align='left' scene='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1' />A template exists for a related button that can be incorporated into Proteopedia pages and behaves similar to green scene link; when the button is pressed it results in coloring of the nucleotides according to the bases {{ColorKey Bases Nucleotides}}. Example: | |||
{{Button Toggle NucleicDrumsColorScheme}} | |||
<br> | |||
<scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1'>Reset</scene> | |||
| |||
| |||
Similarly, for {{Template:ColorKey Purines}}/{{ColorKey Pyrimidines}}:<br> | |||
{{Button Toggle PurinePyrimidineDrumsColorScheme}} | |||
<br> | |||
<scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1'>Reset</scene> | |||
| |||
===Other Color Schemes=== | ===Other Color Schemes=== | ||