Re: [PyMOL] Show hydrogen bonds in current object only
Hi Jason, On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees jason.vertr...@gmail.com wrote: You can automate the task. Load your 100 proteins. Use a wildcard from the command line or a script like loadDir (http://pymolwiki.org/index.php/LoadDir). Align them. Then, run: python for n in cmd.get_names(objects): selName = s + n cmd.select(selName, n) cmd.distance(dist+n, selName, selName + and (organic and + n + ), 3.2, mode=2) python end I'm just curious, but why do you go to the trouble to create a selection that is just the whole object? Especially if Chimed has 100s of objects, he doesn't need to add a named selection for each. Why not do the following? python for n in cmd.get_names(objects): cmd.distance(dist+n,n,n + and organic,3.2, mode=2) python end The latter worked for me. If you wanted to eliminate waters from the selection for the protein, you could change it to: python for n in cmd.get_names(objects): cmd.distance(dist+n,n + and not solvent,n + and organic,3.2,mode=2) python end Or to make it more readable: python for n in cmd.get_names(objects): protein_sele = n + and not solvent organic_sele = n + and organic cmd.distance(dist+n, protein_sele, organic_sele, 3.2, mode=2) python end Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821Fax: 613-533-2497 robert.campb...@queensu.cahttp://pldserver1.biochem.queensu.ca/~rlc -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Show hydrogen bonds in current object only
Robert, Great point! My original script had selections from protein A to a ligand in any other protein B. I just left it in there. I agree that creating a named selection for each object is unnecessary. If he really wanted a clean namespace, he could dump all of those into a group(s) or a multi-state object. Nice attention to detail, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Sun, Nov 29, 2009 at 9:50 PM, Robert Campbell robert.campb...@queensu.ca wrote: Hi Jason, On Sun, 29 Nov 2009 12:29:08 -0500, Jason Vertrees jason.vertr...@gmail.com wrote: You can automate the task. Load your 100 proteins. Use a wildcard from the command line or a script like loadDir (http://pymolwiki.org/index.php/LoadDir). Align them. Then, run: python for n in cmd.get_names(objects): selName = s + n cmd.select(selName, n) cmd.distance(dist+n, selName, selName + and (organic and + n + ), 3.2, mode=2) python end I'm just curious, but why do you go to the trouble to create a selection that is just the whole object? Especially if Chimed has 100s of objects, he doesn't need to add a named selection for each. Why not do the following? python for n in cmd.get_names(objects): cmd.distance(dist+n,n,n + and organic,3.2, mode=2) python end The latter worked for me. If you wanted to eliminate waters from the selection for the protein, you could change it to: python for n in cmd.get_names(objects): cmd.distance(dist+n,n + and not solvent,n + and organic,3.2,mode=2) python end Or to make it more readable: python for n in cmd.get_names(objects): protein_sele = n + and not solvent organic_sele = n + and organic cmd.distance(dist+n, protein_sele, organic_sele, 3.2, mode=2) python end Cheers, Rob -- Robert L. Campbell, Ph.D. Senior Research Associate/Adjunct Assistant Professor Botterell Hall Rm 644 Department of Biochemistry, Queen's University, Kingston, ON K7L 3N6 Canada Tel: 613-533-6821 Fax: 613-533-2497 robert.campb...@queensu.ca http://pldserver1.biochem.queensu.ca/~rlc -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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 -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july ___ 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] Show hydrogen bonds in current object only
Hello PyMol users, I have a lot of pdb files open and I've superposed them to compare the pockets. Now I would like to see the hydrogen bonds formed by each ligand to the protein its been crystalised with. I would ideally like an object which shows hydrogen bonds between the ligand(s) present (I use organic to identify them since the naming is different in each pdb) and the protein of the enabled object. So far I keep getting an object showing all the hydrogen bonds in all the pdbs at once. Given the number of pdbs I'm comparing creating hydrogen bond objects for each of them would be cumbersome. Thank you, Chimed -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ 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
