Mirek, PyMOL isn't the optimal tool for measuring surface area -- perhaps others on the list can suggest good alternatives.
The only kind of surface area PyMOL can measure well is solvent accessible area, and it is a bit slow because all it does is sum up partial areas associated with discrete dots on spheres (size = vdw + solvent radius). The basic approach is: # (1) make sure no atoms are ignored: flag ignore, none # (2) delete everything except what you want to measure (important!): remove not polymer # (3) adjust dot settings for solvent surface area measurement: set dot_solvent, on set dot_density, 4 # (4) visually preview what is being measured (optional): show dots # (5) computer the surface area value: print cmd.get_area() Cheers, Warren > -----Original Message----- > From: Mirek Cygler [mailto:mi...@bri.nrc.ca] > Sent: Monday, August 10, 2009 11:08 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] Measure surface area > > Hi, > How can I get the measure in A2 of the surface area of the surface I > display with PyMol? > > Mirek > > > ------------------------------------------------------------------------ -- > ---- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- > Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > 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 > > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ 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
