From: Warren D. <wa...@de...> - 2009-08-10 18:22:33
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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...@br...] > Sent: Monday, August 10, 2009 11:08 AM > To: pym...@li... > 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 (PyM...@li...) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pym...@li... > > > |
From: Robert C. <rob...@qu...> - 2009-08-10 18:49:40
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Hi Mirek, On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano <wa...@de...> wrote: > PyMOL isn't the optimal tool for measuring surface area -- perhaps > others on the list can suggest good alternatives. I like MSMS for this. I have a script that will calculate the area (both solvent exposed and solvent accessible) for a particular selection. See my msms_pymol.py script at: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol After loading the script with the "run" command, you can type "help calc_msms_area" to get more information on the options. 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 <rob...@qu...> http://pldserver1.biochem.queensu.ca/~rlc |