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=
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?