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The (least) Root Mean Square Deviation is used for comparing different conformations of the same molecule. However one may be interested in comparing the conformations of two different molecules e.g. two proteins of different backbone lengths. So is there any method for comparing conformations different molecules such as a generalized RMDS?

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PyMOL ("align molecule1, molecule2" returns aligned structures and RMSD). TM-align (returns aligned structures and TM-score; tmalign.py is a python module for running TM-align using PyMOL).

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