Michael, You are correct. Users can just download the CE program and use that. The CEAlign that I was talking about is a C++ extension that I wrote just for PyMOL. It plugs directly into the PyMOL system so you can just type: cealign protA, protB and the proteins are aligned and the results are shown in PyMOL. This extension does require either a matching Python distribution that which ships with PyMOL or that you compile PyMOL from source.
Thanks for the note, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Tue, Dec 8, 2009 at 11:12 AM, Michael Zimmermann <micha...@iastate.edu>wrote: > Dr. Vertrees, thank you for the thorough reply to Saeid's question. I just > wanted to note that you don't have to install all of PyMol from source to > use CE. You can set up CE and just run it when you want it, like other > python add-ons. That might not be the case for the most recent version > though, from browsing the wiki link given above... > > > On Tue, Dec 8, 2009 at 9:43 AM, Jason Vertrees > <jason.vertr...@gmail.com>wrote: > >> Saeid, >> >> If you know exactly which atoms in protein A are to be paired with atoms >> in protein B, then this is "fitting" and PyMOL can do it with the "fit" >> family of commands. In PyMOL type, "help fit" to get help and "fit ?" for >> fit's syntax. (A neat trick in PyMOL: "commandName ?" will show you in one >> line how to use that command, eg. "fit_rms ?"). Also, if it's just a few >> atoms, then you can also use PyMOL's pair fitting wizard. Look under the >> Wizard menu. >> >> If you need PyMOL to figure out which atoms to pair together between the >> two proteins, then you need an alignment algorithm before the fitting >> algorithm. PyMOL comes with two standard alignment algorithms "align" and >> "super". If you compile PyMOL from source you can use a third, "cealign". >> >> Possibly useful links: >> http://www.pymolwiki.org/index.php/Intra_Rms >> http://www.pymolwiki.org/index.php/Fit >> http://www.pymolwiki.org/index.php/Cealign >> >> Hope this helps, >> >> -- Jason >> >> -- >> Jason Vertrees, PhD >> >> PyMOLWiki -- http://www.pymolwiki.org >> >> >> On Tue, Dec 8, 2009 at 2:07 AM, saeid mirzaei <smirzae...@yahoo.com>wrote: >> >>> Hi everyone, >>> >>> could some one tell me I can use Pymol for superimposing two protein or >>> not if so how can I use it? >>> >>> Thanks, >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Return on Information: >>> Google Enterprise Search pays you back >>> Get the facts. >>> http://p.sf.net/sfu/google-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 >>> >> >> >> >> ------------------------------------------------------------------------------ >> Return on Information: >> Google Enterprise Search pays you back >> Get the facts. >> http://p.sf.net/sfu/google-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 >> > >
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