[PyMOL] Saving each residue to file
Dear List I was wondering if there could be a way of having every residue of a protein structure being saved to a separate file. How could this be done? I believe the 'iterate' method might be useful in combination with the 'byres' identifier, but I havent figured out how to combine them in the right way. It would be great if the residues could be saved by increasing residue number, something like res-a001 res-f002 where 'a' and 'f' where the residue type and the number is the residue number in the chain. Any hints are very welcome. Martin -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-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
Re: [PyMOL] Saving each residue to file
Hi Martin, there are for sure several ways to achieve this, one might be using the pop command (there is no PyMOLWiki page, but help pop gives a quick example how to use it). fetch 2xwu, async=0 select _justca, byca 2xwu python while cmd.pop(_tmp, _justca): cmd.iterate(_tmp, stored.x='res-'+chain+'-'+resn+resi) cmd.save(stored.x + .pdb, byres _tmp) python end delete _justca _tmp Hope that helps. Cheers, Thomas On 08/15/2011 09:14 AM, Martin Hediger wrote: Dear List I was wondering if there could be a way of having every residue of a protein structure being saved to a separate file. How could this be done? I believe the 'iterate' method might be useful in combination with the 'byres' identifier, but I havent figured out how to combine them in the right way. It would be great if the residues could be saved by increasing residue number, something like res-a001 res-f002 where 'a' and 'f' where the residue type and the number is the residue number in the chain. Any hints are very welcome. Martin -- Thomas Holder MPI for Developmental Biology -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-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
[PyMOL] loading gro files
Hi all, Is there a direct way to load a gromacs structure file (.gro) in PyMOL? I know it's simple to convert them to pdb using editconf, but I want to load gro files directly (as you can in vmd) because they permit higher max. atom and residue numbers (100K vs. 10K for pdb) and permit longer residue names (4 chars vs. 3 for vmd). Thanks, Mike -- Michael D. Daily Postdoctoral research associate Pacific Northwest National Lab (PNNL) 509-375-4581 (formerly Qiang Cui group, University of Wisconsin-Madison) -- uberSVN's rich system and user administration capabilities and model configuration take the hassle out of deploying and managing Subversion and the tools developers use with it. Learn more about uberSVN and get a free download at: http://p.sf.net/sfu/wandisco-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
