Ramesh, You can do something like this...
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 -- mailto:war...@delsci.com Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 > -----Original Message----- > From: pymol-users-ad...@lists.sourceforge.net > [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of > Ramesh Sistla > Sent: Tuesday, July 13, 2004 9:55 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] polar surface area with pymol > > Hi List! > > Is there any way I can calculate the PSA of a molecule with > pymol? Will be grateful for any hints. > > Thanks and regards, > > -- > Ramesh Sistla > Science Fellow > > This email and its attachments are confidential and > proprietary to AURIGENE Discovery Technologies and are meant > for the intended recipient only. If you are not the intended > recipient, do not take any actions based on the contents of > this message, except to permanently delete the message and > its attachments and inform the sender immediately. > > > > > > ------------------------------------------------------- > This SF.Net email sponsored by Black Hat Briefings & Training. > Attend Black Hat Briefings & Training, Las Vegas July 24-29 - > digital self defense, top technical experts, no vendor > pitches, unmatched networking opportunities. Visit > www.blackhat.com _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users >
