Hi Sing, You have a few options.
You can try CASTp (either the web service or the PyMOL plugin). I think the .pocinfo file contains information about volumes. You could also use Voidoo (http://xray.bmc.uu.se/usf/voidoo_man.html). In the distribution, there is a script (cavity.csh) can be used to used to run voidoo to find cavities. The resulting log files have information about volumes. To visualize the cavities, the resulting .ezd files have to bee converted to .ccp4 with mapman. Hope this helps, Xavier Xavier Deupi Laboratory of Computational Medicine Biostatistics Unit. School of Medicine Universitat Autonoma de Barcelona Bellaterra, 08193 (Barcelona) Catalunya, EU lmc.uab.cat On Dec 17, 2009, at 8:16 AM, Kin Sing Stephen Lee wrote: > Dear all, > > I am wondering if it is possible for me to measure the volume of the > binding pocket or the molecule in pymol? If no, any recommend program > for Mac for such purposes? > > Thank you very much > > Sing ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ 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
