View source for 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 [[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 are detailed at the official [http://www.umass.edu/molvis/drums DRuMS website], but are summarized below to show how corresponding color keys can be inserted into the text of Proteopedia pages using templates. The [http://bioinformatics.org/jmol-tutorials Jmol Tutorial-Authoring Template] instructions include a somewhat [http://www.bioinformatics.org/jmol-tutorials/jtat/_docs/jtatdocs.htm#keys1 updated display of the DRuMS color schemes].

===How To Use ColorKey Templates===

For example, to include the ''Composition'' color key for Protein, DNA, and Ligand in your Proteopedia page (omitting the colors for RNA and Solvent, which we'll assume are not shown in the accompanying molecular view), copy this wiki text into the page editing box:

<nowiki>{{Template:ColorKey Composition Protein}}, {{Template:ColorKey Composition DNA}}, {{Template:ColorKey Composition Ligand}}.
</nowiki>

The templates, which work only within Proteopedia, automatically display these terms in boldface. The above will look like this when the page you edited is previewed or saved:

{{Template:ColorKey Composition Protein}}, {{Template:ColorKey Composition DNA}}, {{Template:ColorKey Composition Ligand}}.

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===

This color scheme has five colors:

<big>{{Template:ColorKey Composition Protein}},
{{Template:ColorKey Composition DNA}},
{{Template:ColorKey Composition RNA}},
{{Template:ColorKey Composition Ligand}},
{{Template:ColorKey Composition Solvent}}.</big>

The wiki text to insert the above colored terms is separated into five templates, so that you can insert only the composition terms that apply to the molecular scene at hand. Punctuation, such as commas or periods, can be added after each term if desired. See the above [[#How To Use ColorKey Templates|example]].

<pre>
{{Template:ColorKey Composition Protein}}
{{Template:ColorKey Composition DNA}}
{{Template:ColorKey Composition RNA}}
{{Template:ColorKey Composition Ligand}}
{{Template:ColorKey Composition Solvent}}
</pre>

Proteopedia's ''Scene Authoring Tool'' includes, in the dialog under the '''colors''' tab, a button that colors the currently selected atoms with this color scheme.

===Element===

Carbon, Hydrogen, Oxygen, Nitrogen:
{{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}}
{{Template:ColorKey_Element_Fe}}

The above colored element symbols were generated by including the following Template wikitext blocks:
<pre>
{{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}}
{{Template:ColorKey_Element_Fe}}
</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===
{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}
The above keys were generated by including the following Template wikitext blocks:
<pre>
{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}
</pre>


===Charge===
{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}

The above keys were generated by including the following Template wikitext blocks:
<pre>
{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}
</pre>

===Secondary Structure===
<blockquote><big>
{{Template:ColorKey_Helix}},
{{Template:ColorKey_310Helix}},
{{Template:ColorKey_PiHelix}},
{{Template:ColorKey_Strand}},
{{Template:ColorKey_Loop}},
{{Template:ColorKey_Turn}}.
</big></blockquote>

The above colored terms were generated by including the following Template wikitext blocks:
<pre>
{{Template:ColorKey_Helix}},
{{Template:ColorKey_310Helix}},
{{Template:ColorKey_PiHelix}},
{{Template:ColorKey_Strand}},
{{Template:ColorKey_Loop}},
{{Template:ColorKey_Turn}}.
</pre>

===Rainbows===
These ''Rainbow'' color schemes are not strictly part of DRuMS, but are listed here for convenience.
Amino to carboxy:
{{Template:ColorKey_N2CRainbow}}
<br>
{{Template:ColorKey_Amino2CarboxyRainbow}}
Nucleic acids:
{{Template:ColorKey_523Rainbow}}
Both:
{{Template:ColorKey_N52C3Rainbow}}

The above Rainbow keys were generated by including the following Template wikitext blocks:
<pre>
{{Template:ColorKey_N2CRainbow}}
{{Template:ColorKey_Amino2CarboxyRainbow}}
{{Template:ColorKey_523Rainbow}}
{{Template:ColorKey_N52C3Rainbow}}
</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>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1'>Reset</scene>


&nbsp;
&nbsp;


Similarly, for {{Template:ColorKey Purines}}/{{ColorKey Pyrimidines}}:<br>
{{Button Toggle PurinePyrimidineDrumsColorScheme}}
<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<scene name='User:Wayne_Decatur/kink-turn_motif/Kt7_halo/1'>Reset</scene>

&nbsp;

===Other Color Schemes===

If you would like help constructing a Template for another standard color scheme not listed here, elements not listed above, etc. feel free to email {{Template:Contact}}.

==See Also==

* [[Help:Color_Keys]]