Thanks for your help Jason and David!

I'll have a look at your suggestions, although I solved my problem in a 
different way. I just copied the coordinates of the important symmetry mates 
into the pdb file containing the original molecule of protein B (and set up a 
new chain for each of the sym mates). Superimposing protein B (the chain 
containing the original molecule) on protein A moves all desired sym mates 
according to the movement of the original molecule. 
Anyway, getting the translation / rotation matrix is much more convenient than 
copying all the coordinates... :-)

Thanks once again!

Matthias

> Date: Tue, 19 Jan 2010 07:02:44 -0800
> From: dwash59_2...@yahoo.com
> Subject: Re: [PyMOL]  get translation / rotation matrix from "super"
> To: matze_haf...@hotmail.com; pymol-users@lists.sourceforge.net
> 
> Matthias Haffke said:
> > Is there a way to "extract" the translation / rotation matrix out of the 
> > super command or can I use another command to align both, 
> > protein B and A and to apply the function on every symmetry mate? 
> 
> In addition the commands mentioned by Jason, you can look at matrix_copy
> http://www.pymolwiki.org/index.php/Matrix_copy
> 
> You would align protein B to A, then matrix_copy protein_b, symmetry_mates
> 
> Note, the second argument can have a wild card, so you only need to call the 
> command once to move all of them if they all have a common prefix or the such.
> 
> -David
> 
> 
>       
                                          
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