what about Caver: http://loschmidt.chemi.muni.cz/caver/concept.php very nice and it works very well
andrea 2005/11/7, Bingding Huang <bhu...@biotec.tu-dresden.de>: > > Dear all, > > I download CASTpyMOL.pyc and put it in the right folder. > Now I want to use it for detecting cavity for 50 proteins. I don't want > to do that one after one by hand. > Is it possible to write a python (pymol) script to do that automatically? > > Thanks a lot! > > Regards > Bingding > > > > > > Sebastien Moretti wrote: > > Dear Bingding, > CASTp cavities are pre-computed for most of PDB entries. > > So, you could create a PyMOL script (.pml) which could look like that: > "call the CASTp plugin for xxxx" ? > save xxxx.pdb > reinitialize > "call the CASTp plugin for yyyy" ? > ... > > With this kind of script you could be able to get the cavities for your > 50 proteins with only one PyMOL execution. > Nevertheless, I don't know how to call the CASTp plugin from a PyMOL > script. And how to save all cavities as distinct pdb files. > But I know that that is possible. > > Only the PyMOL mailing list or Wiki are able to help you now. > > > > > > Hi Marcus, > > You can install the CASTp plugin for PyMOL : > > http://cast.engr.uic.edu/cast/?mode=CASTpyMOL > > > > CASTp (http://cast.engr.uic.edu/cast/) is "Computed Atlas of Surface > > Topography of proteins" and analyzes the "Anatomy of Protein Pockets > > and Cavities". > > So, with the plugin, you can get every cavities (pockets), CASTp has > > predicted, automatically. > > > > I hope this will help you. > > > >>> Hello all, > >>> > >>> The surface rendering in PyMOL is quite nice, but I cannot separate > >>> the "branches" of the surface. That is, I would like to view a > >>> large cavity inside of a protein independently from the outer, > >>> solvent accessible surface. Is anyone aware of a means to do this? > >>> > >>> Marcus Collins > >>> > >>> ***************************************************************************** > >>> > >>> Marcus D. Collins > >>> Gruner Biophysics Group, Cornell University Dept. of Physics, > >>> LASSP > >>> (h) 607.347.4720 (w) 607.255.8678 (c) 607.351.8650 > >>> "You have opened a new door, and I share this with you, > >>> for I have been where you are now." > >>> ***************************************************************************** > >> > >> > > > > > -- > Bingding Huang > PhD student > Bioinformatics group > Biotec & Department of Computing > Tazberg 47, 01307 > TU Dresden, Germany > > Tel: 0049 351 46340064 (Office) > Tel: 0049 351 4403368 (Home) > Fax: 0049 351 46340061 > Web: http://www.biotec.tu-dresden.de/~bhuang > E-mail: bhu...@biotec.tu-dresden.de > > > > ------------------------------------------------------- > SF.Net email is sponsored by: > Tame your development challenges with Apache's Geronimo App Server. Download > it for free - -and be entered to win a 42" plasma tv or your very own > Sony(tm)PSP. Click here to play: http://sourceforge.net/geronimo.php > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > -- "La conoscenza libera il genere umano dalla superstizione" J. Watson
