Just to quickly add... probably the easiest way to run CE at the present might be through the new protein comparison tool at RCSB-PDB web site:

http://www.rcsb.org/pdb/workbench/workbench.do

Andreas



On Tue, Dec 8, 2009 at 8:12 AM, Michael Zimmermann <michaelz@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.vertrees@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 <smirzaei56@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,


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