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" radio 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
