Folks,
I have been working on implementing correct vanderwaals dot surfaces. And I have put quite a bit of thought/study into connolley surfaces.
Now that much of it is implemented, I have a few questions.
Q1: Are these things important?
Q2: For a Connolly/Richards/solvent accessible surface, how important is it to change the size of the solvent probe?
The RasMol doc says that it always sets the probe size to 1.2 angstroms ... probably the size of HOH. Is this the only probe size that is interesting?
Q1: Difficult to say. Does the fact that every decent 3D display program has this stuff mean that it is important. Probably not. But who knows.
Certainly the demo screen shots will make the JMol manual much nicer :-)
Q2: By definition, the size of the solvent in which the respective molecule has been dissolved is relevant (surpise :-)).
And for those molecules, for which this kind of stuff might be done, the solvent is water in 99.9% of all cases, I'd say.
This makes is less important to me to be able to change the probe size, but on the other hand, I have the feeling that it might be interesting to see how the SAS of ubiquitin looks in liquid barium :-)
Sorry, not much help, I'm afraid.
Cheers,
Chris
-- Dr. Christoph Steinbeck (e-mail: [EMAIL PROTECTED]) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Zülpicher Str. 47, 50674 Cologne Tel: +49(0)221-470-7426 Fax: +49 (0) 221-470-7786
What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3..
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