From: Harp, J. M <joel.harp@Vanderbilt.Edu> - 2003-11-12 22:10:19
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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 |
From: Maria L. R. <mlr...@ig...> - 2009-04-21 16:02:46
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Dear all, Is there any PyMOL command to calculate surface areas? Many thanks, Luisa Rodrigues |
From: Folmer F. <fo...@gm...> - 2009-04-21 16:23:49
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Dear Luisa, 2009/4/21 Maria Luisa Rodrigues <mlr...@ig...>: > Dear all, > > Is there any PyMOL command to calculate surface areas? > Many thanks, > Did you try to search for information yourself first? Anyways, the pymolwiki.org is always a good place to go and then you would have found something like this: http://pymolwiki.org/index.php/Get_Area I hope this is what you are looking for? Best regards, Folmer Fredslund |
From: Kaushik R. <kx...@ps...> - 2003-11-12 22:54:54
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To calculate surface area for a defined object from the PyMOL command=20 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?=A0 For instance, can it calculate surface area occupied by=20 > arginines. > > Thanks, > Joel > > Joel M. Harp > Vanderbilt University > |
From: Warren L. D. <wa...@de...> - 2003-11-12 23:08:04
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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:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -----Original Message----- From: pym...@li... [mailto:pym...@li...] On Behalf Of Kaushik Raha Sent: Wednesday, November 12, 2003 2:50 PM To: Harp, Joel M Cc: pym...@li... 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 |
From: Warren L. D. <wa...@de...> - 2003-11-12 23:03:26
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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:wa...@de... Warren L. DeLano, Ph.D. Principal Scientist DeLano Scientific LLC Voice (650)-346-1154 Fax (650)-593-4020 -----Original Message----- From: pym...@li... [mailto:pym...@li...] On Behalf Of Harp, Joel M Sent: Wednesday, November 12, 2003 2:10 PM To: pym...@li... 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 |
From: Kaushik R. <kx...@ps...> - 2003-11-12 23:41:49
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Hi Warren, I found out that it is possible to write out AMBER style atom name formats with hydrogens added using the Chempy which is pretty neat. However it seems like this does not recognize the N-terminal residue for adding hydrogens. Is that still the case? I am still using PyMOL 088 (I will soon upgrade). Thanks, Kaushik. -- Graduate Student Penn State University University Park PA-16801 |