Re: [PyMOL] Alignment Objects
Hi David On Thu, 10 Sep 2009 14:47:43 -0700 (PDT) David Hall dwash59_2...@yahoo.com wrote: Is there any documentation on getting information out of alignment objects into scripts? I tried looking around the wiki, but I didn't see anything. I'm just wondering things like if I have a residue in one object, finding the residue in another object that has been aligned. If you create an alignment object when you do the alignment: align proteinA, proteinB, object=A_on_B then you can save a clustal formatted alignment file by typing: save A_aligned_with_B.aln, A_on_B (same applies if you use the super command instead of align). 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] Alignment Objects
Hi, Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? Maia -- 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] Alignment Objects
Maia, select all_arg_lys, resn arn+lys Cheers, Warren -Original Message- From: Maia Cherney [mailto:ch...@ualberta.ca] Sent: Friday, September 11, 2009 2:03 PM To: pymol-users@lists.sourceforge.net Subject: Re: [PyMOL] Alignment Objects Hi, Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? Maia -- 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
Re: [PyMOL] Alignment Objects
On Fri, Sep 11, 2009 at 1:59 PM, Maia Cherney ch...@ualberta.ca wrote: Is it posible in pymol to select all residues of a certain type automatically, like all arginines or all lysines + arginines in a chain? select resnam arg select chain A and (resnam lys or resnam arg) -- 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] Alignment Objects
Is there any documentation on getting information out of alignment objects into scripts? I tried looking around the wiki, but I didn't see anything. I'm just wondering things like if I have a residue in one object, finding the residue in another object that has been aligned. Thanks, David -- 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] Alignment objects
Dear PyMOL community, I am trying to use the align command (from within python) and want to evaluate the pairwise matches. the command cmd.align(sel1, sel2, object=alignment) should do. Sorry for this stupid question, but how do I get hold of the alignment object, and what is its functionality? Ie which methods/values does it provide? Many thanks. Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063
RE: [PyMOL] Alignment objects
Andreas, It's not a stupid question -- its just a year or more ahead of its time. Right now aligment objects currently don't do anything other than show you which atoms were aligned in the 3D viewer. In time however, those objects will integrate with the sequence-viewer... Cheers, Warren -Original Message- From: pymol-users-ad...@lists.sourceforge.net [mailto:pymol-users-ad...@lists.sourceforge.net] On Behalf Of Andreas Henschel Sent: Friday, January 28, 2005 9:18 AM To: pymol-users@lists.sourceforge.net Subject: [PyMOL] Alignment objects Dear PyMOL community, I am trying to use the align command (from within python) and want to evaluate the pairwise matches. the command cmd.align(sel1, sel2, object=alignment) should do. Sorry for this stupid question, but how do I get hold of the alignment object, and what is its functionality? Ie which methods/values does it provide? Many thanks. Andreas -- Andreas Henschel Bioinformatics Group TU Dresden Tatzberg 47-51 01307 Dresden, Germany Phone: +49 351 463 40063 --- This SF.Net email is sponsored by: IntelliVIEW -- Interactive Reporting Tool for open source databases. Create drag--drop reports. Save time by over 75%! Publish reports on the web. Export to DOC, XLS, RTF, etc. Download a FREE copy at http://www.intelliview.com/go/osdn_nl ___ PyMOL-users mailing list PyMOL-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/pymol-users
