One program which can do this is SURFNET: http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html
There are two ways in which cavities can be displayed: i) SURFNET can write out PDB format files containing the atoms/residues lining each cleft, which you can view directly ii) If linked with the CCP4 libraries when compiled, SURFNET can write CCP4 format density maps which describe the shape of each cavity. These can be loaded into PyMOL and contoured to show the location of each cleft. HTH Gareth On Thu, 2004-07-22 at 14:28, Dirk Kostrewa wrote: > Dear PyMol users, > > I'm looking for a program that can calculate and write out cavities in a > format that can be converted such that I can display it with PyMol (I'm not > satisfied with the results from VOIDOO). Could you please send me any pointer > to a program that you found useful? BTW, this would be my wish for a next > release of PyMol! > > Best regards, > > Dirk. -- Gareth Stockwell European Bioinformatics Institute
