Hi Ormus, Not sure if this can easily be done in PyMol, but I used HydroNMR and HydroPro for something similar for the process of analysing the hydrodynamic properties of molecules. As far as I remember they don't work with overlapping spheres but fill the space of a molecule with spheres of equal size.
See Torre, Huertas and Carrasco (2000) Journal of Magnetic Resonance, 147, 138pp or http://leonardo.fcu.um.es/macromol/programs/hydronmr/hydronmr.htm Peter -- Dr Peter Teriete Laboratory of Molecular Biophysics Department of Biochemistry University of Oxford South Parks Rd. Oxford OX1 3QU Tel: +44 1865 275742 Fax: +44 1865 275182 -----Original Message----- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of ormus cama Sent: 05 August 2005 01:04 To: pymol-users@lists.sourceforge.net Subject: [PyMOL] volume approximation hi, i am looking for some advice. i would like to create a set of overlapping spheres whose combined volume approximates the actual volume of a protein of interest. obviously, i am looking for a reduced representation. ideally, i am talking about no more than a handful of spheres. these spheres should all be equally sized and the degree of overlap between spheres should be consistent across all of them (that is, they should all overlap all neighboring spheres equally). i'm trying to construct an algorithm that would take in the pdb coordinates of the protein to be approximated and output a set of points corresponding to the origins of the spheres required to fill the volume of the original protein to some determined degree of accuracy (eg. > 90%). i'm relatively new to pymol, but of all the molecular visualization programs i have looked at, it seems best suited to the task at hand. has anyone done anything even remotely like this? can anyone offer insight as to whether i can do this within pymol and, if so, where i might look (wiki, documenation, etc) to get started? thanks in advance, ormus -- India.com free e-mail - www.india.com. Check out our value-added Premium features, such as an extra 20MB for mail storage, POP3, e-mail forwarding, and ads-free mailboxes! ------------------------------------------------------- SF.Net email is Sponsored by the Better Software Conference & EXPO September 19-22, 2005 * San Francisco, CA * Development Lifecycle Practices Agile & Plan-Driven Development * Managing Projects & Teams * Testing & QA Security * Process Improvement & Measurement * http://www.sqe.com/bsce5sf _______________________________________________ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
