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!
> Date: Tue, 19 Jan 2010 07:02:44 -0800 > From: email@example.com > Subject: Re: [PyMOL] get translation / rotation matrix from "super" > To: firstname.lastname@example.org; email@example.com > > 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 > > >