I wonder what is the best way to superpose two multi-chain proteins, and explicitly specify the chains to include in superposition. I know that I can read only the wanted chains into the alignment, but I also want to make sure that the other chains move according to the superposition.
Here are two ways we could think of: 1. read only the wanted chains and do superposition. Then move the other chains accordingly using functions like selection.rotate_origin(), selection.rotate_mass_center() and selection.transform().
2. model1 <= all chains in protein A model2 <= all chains in protein B model3 <= the chain(s) selected for superposition in protein B first, superpose model3 to model1 (model3 is moved) second, superpose model2 to model3 (model2 is moved)
Are there any better ways? Thank you.