I wanted to have a program that can easily calculate cavities in proteins to be displayed with pymol (see e-mails below for details). Thanks to Gareth and Lari I've got two pointers to such programs: I've tried PASS, recommended by Lari and got a surface picture of my cavities within literally a few minutes, as Lari already wrote. I've ordered SURFNET, recommended by Gareth and will also try it (it needs a signed license agreement returned by mail).
Many thanks again! Best regards, Dirk. Gareth Stockwell wrote: > One program which can do this is SURFNET: > > http://www.biochem.ucl.ac.uk/~roman/surfnet/surfnet.html > > There are two ways in which cavities can be displayed: > > i) SURFNET can write out PDB format files containing the atoms/residues > lining each cleft, which you can view directly > > ii) If linked with the CCP4 libraries when compiled, SURFNET can write > CCP4 format density maps which describe the shape of each cavity. These > can be loaded into PyMOL and contoured to show the location of each > cleft. > > HTH > Gareth Lari Lehtiö wrote: > I was looking for such a program couple of days ago, and I found "pass". > > http://www.ccl.net/cca/software/UNIX/pass/overview.shtml > > I saw the cavities in couple of minutes in pymol :) I'm not familiar with > voidoo, so I don't know if you will find this usefull or not... > > My current problem is related to this one, so I'll post it here also. > I would like to calculate surface of the cavity with pymol and show this as > a cavity going in to the protein. But the surface is all grey, because it > is the "inside". Is there a way to map the colours also to the other side > of the surface? > > best regards, > > ~Lari~ > > > »»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»» > Lari Lehtiö > University of Helsinki > Institute of Biotechnology > Macromolecular X-ray crystallography > P.O.Box 65 > 00014 HY > Finland > »»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»»» > Quoting Dirk Kostrewa <dirk.kostr...@psi.ch>: > > # Dear PyMol users, > # > # I'm looking for a program that can calculate and write out cavities in a > # > # format that can be converted such that I can display it with PyMol (I'm > # not > # satisfied with the results from VOIDOO). Could you please send me any > # pointer > # to a program that you found useful? BTW, this would be my wish for a > # next > # release of PyMol! > # > # Best regards, > # > # Dirk. > # > # -- > # > # **************************************** > # Dirk Kostrewa > # Paul Scherrer Institut > # Life Sciences, OFLC/110 > # CH-5232 Villigen PSI, Switzerland > # Phone: +41-56-310-4722 > # Fax: +41-56-310-5288 > # E-mail: dirk.kostr...@psi.ch > # http://sb.web.psi.ch > # **************************************** > # > # > # > # ------------------------------------------------------- > # This SF.Net email is sponsored by BEA Weblogic Workshop > # FREE Java Enterprise J2EE developer tools! > # Get your free copy of BEA WebLogic Workshop 8.1 today. > # http://ads.osdn.com/?ad_id=4721&alloc_id=10040&op=click > # _______________________________________________ > # PyMOL-users mailing list > # PyMOL-users@lists.sourceforge.net > # https://lists.sourceforge.net/lists/listinfo/pymol-users > # -- **************************************** Dirk Kostrewa Paul Scherrer Institut Life Sciences, OFLC/110 CH-5232 Villigen PSI, Switzerland Phone: +41-56-310-4722 Fax: +41-56-310-5288 E-mail: dirk.kostr...@psi.ch http://sb.web.psi.ch ****************************************
