From: Piter_ <x....@gm...> - 2006-04-04 10:15:41
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Dear all. I need to select surface atoms. Friend of mine recommended me this way: For solvent accessible surface one can try Molmol: Load your molecule, say " SelectAtom '' " in command line, say "CalcSurface= " - select the solvent radius (1.4A for water by default), put "by atom" radi= o button on and then save and import the text output into spreadsheet of your choice. Unfortunately output has solvent accessibility data for all the atoms of the molecule - you use spreadsheet to filter those atoms which are exposed most (i.e. - on the surface of the molecule). In case you need a VdW surface you can try to decrease the solvent radius. After that I selected needed atoms in command line. Is is possible to do it everything in pymol and automatically? Thanks Petro |