Hi Sujuan, On Tue, 18 May 2010 15:58:59 +0800 sujuan wang <wsjpy...@gmail.com> wrote:
> thank you for you reply and modification of the script. now Ican calculate > the surface area. but when I calculate the surface of part protein, it seem > that the surface area including the surface adjacent with other residues, > means the sum of two fragments is much larger than whole protein surface, is > there any method to calculate the surface only exposure to solvent? I'm not sure I understand your problem. Are you trying to calculate an interface surface, such as between two proteins or between two chains of one protein? Normally the msms program will only calculate the surface that is exposed to solvent. The script reports two values for area, the solvent excluded surface (otherwise known as the molecular surface -- similar to what is displayed by PyMOL when you show the surface) and the solvent accessible surface. The latter is the surface traced out by the centre of a water-sized probe as it rolls over the van der Waals surface of the protein. It is therefore larger than the solvent excluded surface. Perhaps you could send me at least the output from the calc_msms_area command to show me what you mean. Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
