This is not what I wanted to achieve. And everyone else who is interested in this kind of information (the solvent accessible surface) may hit me now (but only one or two times).
Miguel, I'm not the right person to ask for that kind of information (and accordingly I should shut up and not anwser your questions - that's correct). Please wait for some other replies before making yourself a picture about the importance of SAS's
And honestly, I think the algorithm for calculating this surface *efficiently* is quite intersting.
Cheers,
Chris
Miguel wrote:
Jmol developers,
I just checked in code which implements rendering of vanderwaals dot surfaces.
After Christoph's *inspiring* report I must admit that I am somewhat less enthusiastic about implementing the solvent accessible surface :( But the screen rendering of vdw dot surfaces *does* look pretty good. We'll see.;^)
Miguel
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,
-- Dr. Christoph Steinbeck (e-mail: [EMAIL PROTECTED]) Groupleader Junior Research Group for Applied Bioinformatics Cologne University BioInformatics Center (http://www.cubic.uni-koeln.de) Z�lpicher 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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