Dear Buz, On Fri, 04 Jan 2008 15:43:41 -0500, Buz Barstow <b...@mac.com> wrote:
> Dear all, > > I'd like to very accurately calculate the volume of a selection in > pymol, or with tools that are callable by pymol? Could anyone suggest > a program or algorithm? MSMS will calculate areas and volumes. I have written a python script that you can run from within PyMOL to call msms. You can find it (msms_pymol.py) at my scripts web page: http://pldserver1.biochem.queensu.ca/~rlc/work/pymol It does not use the pdb_to_xyzrn script supplied with msms -- that conversion is now built in to the python script. After "running" the script to load it, then you can do: calc_msms_area object_name with options for changing the selection for calculating the area, the probe radius and density. Because I was most interested in the calculation of surface areas, including buried surface areas, the initial MSMS calculation is only run on the complete object. That is what volume will be reported. For example, to calculate the surface area of chain A of a protein that is buried by chain B, first create two objects: create protein_A, protein & chain A create protein_B, protein & chain B Then run: calc_msms_area protein_A,protein_A within 4. of protein_B,probe=1.4 This will therefore report the volume of all of protein_A, but for the surface areas, only the part of A that is buried by B. 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 <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc
