Hi... Let's say I want to compare the same protein crystallized in different conditions. Same space group, almost same resolution. The global RMSD will be pretty small (around 0.3 Angstroms). There will be some changes in rotamers in some residues and some extra waters here and there... Besides local rsmd and contact maps (or differences in contact maps)... is there anything else to get a decent view of these small changes?
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