DRuMS

From Proteopedia

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Contents 1 What is DRuMS? 2 The DRuMS Color Schemes 2.1 How To Use ColorKey Templates 2.2 Composition 2.3 Element 2.4 Hydrophobic/Polar 2.5 Charge 2.6 Secondary Structure 2.7 Rainbows 2.8 Additional DRuMS ColorKey Templates 2.9 Other Color Schemes 3 See Also

What is DRuMS?

DRuMS refers to a set of standard color schemes for macromolecular visualization, released in 2000. The official DRuMS website is 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 Jmol Colors), Chime, Protein Explorer, the Jmol Tutorial-Authoring Template, and 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: Timothy Driscoll, Frieda Reichsman, Eric Martz, and Roger A. Sayle (author of RasMol).

The DRuMS Color Schemes

The DRuMS color schemes are detailed at the official DRuMS website, but are summarized below to show how corresponding color keys can be inserted into the text of Proteopedia pages using templates. The Jmol Tutorial-Authoring Template instructions include a somewhat 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:

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

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:

Protein, DNA, Ligand.

If you enclose the wiki text in <span style="font-size:150%">...</span> tags, it will look like this:

Protein, DNA, Ligand.

Composition

This color scheme has five colors:

Protein, DNA, RNA, Ligand, Solvent.

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 example.

{{Template:ColorKey Composition Protein}}
{{Template:ColorKey Composition DNA}}
{{Template:ColorKey Composition RNA}}
{{Template:ColorKey Composition Ligand}}
{{Template:ColorKey Composition Solvent}}

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: C H O N P S Se Fe

The above colored element symbols were generated by including the following Template wikitext blocks:

{{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}}

If you need additional elements, simply create the appropriate Template page, using Jmol Colors, or contact . Be sure to include additional elements in the lists above.

Hydrophobic/Polar

Hydrophobic, Polar The above keys were generated by including the following Template wikitext blocks:

{{Template:ColorKey_Hydrophobic}},  {{Template:ColorKey_Polar}}

Charge

Anionic (-) / Cationic (+)

The above keys were generated by including the following Template wikitext blocks:

{{Template:ColorKey_Charge_Anionic}} / {{Template:ColorKey_Charge_Cationic}}

Secondary Structure

Alpha Helices, 3₁₀ Helices, Pi Helices,  Beta Strands ,  Loops , Turns.

The above colored terms were generated by including the following Template wikitext blocks:

{{Template:ColorKey_Helix}},
{{Template:ColorKey_310Helix}},
{{Template:ColorKey_PiHelix}},
{{Template:ColorKey_Strand}},
{{Template:ColorKey_Loop}},
{{Template:ColorKey_Turn}}.

Rainbows

These Rainbow color schemes are not strictly part of DRuMS, but are listed here for convenience. Amino to carboxy:

N

C

Amino Terminus

Carboxy Terminus

Nucleic acids:

5'

3'

Both:

N, 5'

C, 3'

The above Rainbow keys were generated by including the following Template wikitext blocks:

{{Template:ColorKey_N2CRainbow}}
{{Template:ColorKey_Amino2CarboxyRainbow}}
{{Template:ColorKey_523Rainbow}}
{{Template:ColorKey_N52C3Rainbow}}

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:
Azure, Crimson, Green, Tweety Bird, Umber.

Purines, Pyrimidines,
A C G T U,
A C G T,
A C G U.

The above colored terms were generated by including the following Template wikitext blocks:

{{Template:ColorKey Purines}}
{{Template:ColorKey Pyrimidines}}
{{Template:ColorKey Bases Nucleotides}}
{{Template:ColorKey Bases DNA}}
{{Template:ColorKey Bases RNA}}

spinqualitylabelsall models Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

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 A C G T U. Example:

           

   

Similarly, for Purines/Pyrimidines:

           

 

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 .

See Also

• Help:Color_Keys