I was wondering if this problem was exclusive for my case. I was using "pair_fit" (rather than super/align) to superimpose two conformations of the same structure and noticed two things:
1) After being superimposed, BOTH structures (source and target) end up moving rather than just one
2) The object matrix is not changed from identity for either source or target structures (even though both structures have moved)
My question is whether there is a way to avoid having both structures move and only have the target move towards the source? If not, is there a way to ensure that the object matrix for both structures get updated after they are shifted?