Re: [PyMOL] selecting side chains
Hi, * Lisa Craig licr...@sfu.ca [2005-01-27 20:43] wrote: How do I select side chains without selecting the backbone atoms? Add ! n. n+ca+c+o or in long form and not name n+ca+c+o to your selection. So to colour all arginine and lysine side chains blue: color blue, r. arg+lys ! n. n+ca+c+o Cheers, Rob -- Robert L. Campbell, Ph.D. r...@post.queensu.ca Senior Research Associatephone: 613-533-6821 Dept. of Biochemistry, Queen's University, fax: 613-533-2497 Kingston, ON K7L 3N6 Canada http://adelie.biochem.queensu.ca/~rlc PGP Fingerprint: 9B49 3D3F A489 05DC B35C 8E33 F238 A8F5 F635 C0E2
[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
[PyMOL] combining models in a biounit
hi, i want to combine the models in a biounit file. for example, ftp://ftp.rcsb.org/pub/pdb/data/biounit/coordinates/divided/ky/1kyw.pdb2.gz has two models. so, i - load it - split_states on it - save everything into a pdb file but .. the pdb file ends up empty (it's just an END line). am i doing something wrong? is there a workaround? thanks, -michael -- This isn't a democracy;|_ |Michael Lerner it's a cheer-ocracy. | ASCII ribbon campaign ( ) | Michigan -Torrence, Bring It On| - against HTML email X | Biophysics | / \ | mler...@umich
