Warren, I've used Varshney's surface code (written at UNC) for many years now. There are some legal statements but I checked with UNC and they told me they didn't care who used copied or modified the code, so I consider it public domain at this point. I would be happy to send you a copy. It is C-code that can actually run in parallel and is quite fast. The surface is the true solvent contact surface (piecewise spheres and tori). It has a couple minor problems that are solvable:
1. poor/degenerate triangulation in a few places 2. needs better dynamic memory management I would be happy to send you a copy of the code. Sorry I have not time to work with PyMol yet, perhaps someday. Richard Gillilan MacCHESS "DeLano, Warren" wrote: > Now, on to Alan's specific questions: > > > I'm particularly interested in how pymol generate surface (a > > internal algorithm?) and how to compare it to vdW, solvent, > > Connolly and > > MSMS surfaces. > > PyMOL's surfacing algorithm is just something I cooked up over a weekend > a couple years back. It is brute-force: 1. surface the atoms, 2. > surface waters in contact with those atoms, and 3. merge the result into > a continuous surface and try to cover up any glitches. If a better (ie. > faster) surfacing algorithm ever enters the public domain/BSD-licecnse > software pool, then I would love to include it as an alternative. > > To get a better surface, select "Maximum Quality" from the "Display" > menu, a go get a cup of coffee while you wait : ). You may need extra > RAM too... > > To make it transparent, "set transparency=1" > > Cheers, > Warren > > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users
