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:

Hope this helps,

-- Jason

Jason Vertrees, PhD

PyMOLWiki --

On Tue, Dec 8, 2009 at 2:07 AM, saeid mirzaei <> 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?

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