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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