On Sep 20, 2006, at 9:27 AM, Angel Herraez wrote:
> Tim,
>
> Sorry, I messed up the URL. This is it:
> http://biomodel.uah.es/en/model3j/index.htm
>
will look at it...
>>> Enter any of the protein sections on the right pane, the click on
>>> "Color schemes" at the bottom
>>> and give any ideas.
>
>> the Chime scripts should just work in Jmol, for the most part; they
>
> Yes, but there are color differences, at least.
> Also, Jmol differentiates DNA from RNA.
>
the original scripts had the DNA/RNA difference in place, as a hack,
but you're right - it is certainly cleaner in Jmol. color
differences are not related to Chime v Jmol per se, but personal
preference. some folks do change the codes, of course (Eric has done
as much with the DRuMS implementation in FirstGlance, I believe).
I know this all sounds trivial, but my point is that the original
package, though implemented in Chime, should work for Jmol without
much bother for the end-user. at least, it does for me. :-)
> Let me work it out in a few days and clean up the js and css files.
> Meanwhile, if you have suggestions on my current implementation, they
> will be welcome.
>
ok, cool.
> I think when we have a defined set, we might ask for commands, but
> which ones will be needed? e.g.:
> - color drumsElements
> - color drumsMacroMicroMolecules
> - color drumsPolarity { 2 / 3 / 5 / 6 }
> - color drumsNucleotides
> - color drumsNucleotidesBackbone
> - color drumsPurinesPyrimidines
>
> just thinking aloud...
>
or this:
color drums [scheme]
where scheme is one of:
element molecule polarity2 polarity3 polarity5
polarity6 nucleic base baseclass
the default (i.e., when no scheme is provided) could be element.
best,
tim
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