Just to throw my 2 cents in following Warren's invitation, I think Mark Gerstein's programs work well for this (calcsurf.exe or something...they're on his web site) ccp4's areaimol does something similar, though I can't recall whether its output was atom by atom. In either case, you may have to add up the component atom parts if you want residue by residue.
Despite Warren's comment, I think last time I was doing this Pymol's results compared well with the above methods, but that was for large areas of a protein interface and perhaps if you want very fine residue level resolution you'd heed his caveat. I though, which is reiterated in the notes accompanying a former post of his... -Seth if I may quote Warren: For a solvent accessible PSA approximation: set dot_density, 3 remove hydro remove solvent show dots set dot_solvent, on get_area elem N+O get_area elem C+S get_area all For molecular PSA approximation set dot_density, 3 remove hydro remove solvent set dot_solvent, off get_area elem N+O get_area elem C+S get_area all Showing dots isn"t mandatory, but it"s a good idea to confirm that you"re getting the value for the atom dot surface you think you"re using. Please realize that the resulting numbers are only approximate, reflecting the sum of partial surface areas for all the dots you see. To increase accuracy, set dot_density to 4, but be prepared to wait... Cheers, Warren ----------------------------------------------------------------------------------------------- Melanie, At present, PyMOL isn't the right tool for this, but perhaps someone on the mailing list will know what is... Cheers, Warren -- Warren L. DeLano, Ph.D. Principal Scientist . DeLano Scientific LLC . 400 Oyster Point Blvd., Suite 213 . South San Francisco, CA 94080 USA . Biz:(650)-872-0942 Tech:(650)-872-0834 . Fax:(650)-872-0273 Cell:(650)-346-1154 . mailto:war...@delsci.com > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Melanie Rogers > Sent: Monday, April 03, 2006 10:36 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Angstrom-squared values for solvent/protein > contact surface per residue > > Dear Pymol Users, > > Is it possible to extract numerical values, (i.e. Angstrom-squared per > residue) > for the solvent/protein contact surface for individual > residues in a crystal structure using Pymol? > > Thank you, > > Melanie Rogers > University of Leeds > >
