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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