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
