Close, but it depends on whether you want the surface area of the residues alone, or in the context of the molecule.
load protein.pdb get_area resn arg will be less than create arg_object, resn arg get_area arg_object This is because the first example will give you only the exposed area of the arginines in the presence of the other atoms, whereas the second gives the area of the arginines in isolation. Cheers, Warren -- mailto:war...@delanoscientific.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 Kaushik Raha Sent: Wednesday, November 12, 2003 2:50 PM To: Harp, Joel M Cc: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] surface area calculation To calculate surface area for a defined object from the PyMOL command line type: print cmd.get_area("obj") where obj is the name of your object. for arginines: create ARG, resn ARG print cmd.get_area("ARG") Kaushik. On Wednesday, November 12, 2003, at 05:10 PM, Harp, Joel M wrote: Is it possible to get pymol to calculate surface area for a defined object? For instance, can it calculate surface area occupied by arginines. Thanks, Joel Joel M. Harp Vanderbilt University
