Joel, Yes, PyMOL does have this capability, but it is immature and not routinely validated. The basic concepts are: 1) "get_area selection" command will return the effective surface area of the dots that you would see from "show dots, selection". This is a discrete approximation -- not an exact calculation. 2) you can use the "dot_solvent" setting to control whether you get solvent surface area or a molecular surface area. 1=solvent, 0=molecular 3) the accuracy of the measurement depends on the density of dots, which is controlled by the "dot_density" setting (1-4). 4) the solvent radius is controlled by the "solvent_radius" setting (default 1.4). For example: PyMOL> load $TUT/1hpv.pdb PyMOL> show dots, resn arg PyMOL> get_area resn arg cmd.get_area: 1147.956 Angstroms^2. PyMOL>set dot_solvent, on PyMOL>get_area resn arg cmd.get_area: 673.084 Angstroms^2. PyMOL>set dot_density, 3 PyMOL>get_area resn arg cmd.get_area: 674.157 Angstroms^2. PyMOL>set dot_density, 4 PyMOL>get_area resn arg cmd.get_area: 672.056 Angstroms^2. PyMOL>get_area all cmd.get_area: 13837.804 Angstroms^2. This code has not been recently validated (though I did check it a couple years back), so I would suggest that people perform some kind of independent check on their system before trusting the results. 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 Harp, Joel M Sent: Wednesday, November 12, 2003 2:10 PM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] surface area calculation 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
