[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
Re: [PyMOL] Measure surface area
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
Re: [PyMOL] Measure surface area
Hi Mirek, On Mon, 10 Aug 2009 11:21:39 -0700 Warren DeLano war...@delsci.com 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: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- 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
