At 5/29/05, Nicolas Vervelle wrote:
is the DRuMS color schemes widely used ?
Thanks for your reply, Nicolas.
The name "DRuMS" (http://www.umass.edu/molvis/drums/) comes from Driscoll,
Reichsman, Martz and Sayle.
The core color schemes in DRuMS (elements, secondary structure) are those
in RasMol (authored by Roger Sayle) and therefore also in Chime (because
its rendering code is adapted from RasMol's public domain source). (See my
recent revision of http://wiki.jmol.org/JmolScripting )
Driscoll (with Reichsman and Martz) extended these core schemes to be
comprehensive, adding schemes for macromolecule type (protein vs. DNA vs.
RNA vs. solvent vs. hetero), amino acid sidechain polarity/charge, purines,
pyrimidines, DNA backbone, RNA backbone, and nucleotide bases. The schemes
were carefully designed so that any combination of schemes can be used
concurrently yet all colors are distinct.
The DRuMS core schemes are built into RasMol and Chime. Full DRuMS is used
by ProteinExplorer.Org (see the "Colored by DRuMS" button/link on its
FrontDoor page), and in Chime-based tutorials for the popular Lehninger
Principles of Biochemistry text, tutorials authored by Driscoll and
Reichsman (http://www.worthpublishers.com/lehninger3d/index2.html). In my
personal opinion, these tutorials (which I was not involved in authoring)
set a high standard of scientific and pedagogic quality.
The figures in each major biochemistry textbook (including Lehninger's) use
different, and often internally inconsistent, color schemes. There is no
agreed-upon standard for macromolecular colors, or for nucleotide base
colors in sequences, and many different schemes are in wide use. DRuMS was
proposed in 2000 partly because of the need for rational color schemes that
could be used concurrently, and partly in response to this chaos in the field.
The DRuMS color schemes, http://www.umass.edu/molvis/drums/ , are supported
by downloadable Chime scripts, cascading style sheets for color-matched
HTML, color charts with RGB codes, demonstration examples, and explicit
rationales. To my knowledge, DRuMS is the only set of macromolecular color
schemes with a website, or with this level of documentation and support.
This is why I proposed that it be linked to the jmol "Colors" page. As time
permits, ideally the whole DRuMS site could be jmol-ized and added to
jmol.sourceforge.net. For now, I recommend a link to the existing site
http://www.umass.edu/molvis/drums/ .
-Eric
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