[PyMOL] protein interaction surface
Hello pymol users, can you help me please how to calculate interaction surface between 2 subunits of my protein? I found this website http://crick.mbu.iisc.ernet.in/~PIC/index.html, but I would rather use pymol if possible. Thanks a lot, Tomas -- S pozdravy T. Kučera -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] protein interaction surface
Hi Tomas, I found this website http://crick.mbu.iisc.ernet.in/~PIC/index.html, but I would rather use pymol if possible. I suggest you only use PyMOL to visualize the results of a validated calculation, or use it to run a script/program that performs the calculation and then view the results. At this time, PyMOL does not have any validated, built in features to do this detection. can you help me please how to calculate interaction surface between 2 subunits of my protein? Having said that, if you simply need something for visualization there are simple scripts on the PyMOLWiki that might help. For example, I wrote InterfaceResidues.py (http://www.pymolwiki.org/index.php/InterfaceResidues) to use difference of surface area to find possible interface residues. This was not validated, surely has lots of scientific holes, and only exists to make visualization easier in PyMOL. Cheers, -- Jason -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] protein interaction surface
Hi Tomas, have you checked PISA? http://pdbe.org/pisa You can also run PISA locally, it's part of the CCP4 suite (however, the output is not that easy to parse). http://www.ccp4.ac.uk/ Cheers, Thomas 2011/3/14 Tomáš Kučera: Hello pymol users, can you help me please how to calculate interaction surface between 2 subunits of my protein? I found this website http://crick.mbu.iisc.ernet.in/~PIC/index.html, but I would rather use pymol if possible. Thanks a lot, Tomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] protein interaction surface
Hi Tomas, for structures from the PDB, PISA offers you XML download. Example: http://www.ebi.ac.uk/msd-srv/pisa/cgi-bin/interfaces.pisa?2x19 You could write a python script to load these results into PyMOL. Cheers, Thomas 2011/3/14 Tomáš Kučera: Hello, yes, I tried pisa, works great, but how can I visualise the output from pisa in pymol? I am not able to download residue list which are in interface, I can see just table where are interface residues marked. Tomas Dne 14. března 2011 14:56 Thomas Holder spel...@users.sourceforge.net napsal(a): Hi Tomas, have you checked PISA? http://pdbe.org/pisa You can also run PISA locally, it's part of the CCP4 suite (however, the output is not that easy to parse). http://www.ccp4.ac.uk/ Cheers, Thomas -- Thomas Holder MPI for Developmental Biology Spemannstr. 35 D-72076 Tübingen -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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] delete an hb from a multiple hb object
Hi Jason, I generated hbs from mode=2 method. It made some wrong hbs. How can I delete those wrong hbs? Maia -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ 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
