I was wondering if there is a way to get a translation / rotation matrix out of the "super" command. My problem is, that I want to superimpose 2 proteins (lets say protein B superimposed on protein A), but I also want to use the same superposition (e.g. the same translation and the rotation function / matrix) for every symmetry mate of protein B. 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?
Both proteins don't have to be aligned perfectly, it's much more important for me to keep the symmetry operations of protein B. I already tried to use the "translate" function to get a sort of alignment (which could then be applied to all symmetry mates), but I wasn't very successful. Looks like the translate function works in respect of your viewing point but not in respect of the cell axis?!?