From: James S. <jms...@gm...> - 2016-06-13 13:42:05
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Dear Pymol users! I am studying protein-protein assosiation using 2 different proteins as test case by means of variety of computational methods. For my particular caseI need to compare binding poses emerged as the result of protein-protein docking (ensemble 1: which consists of 20 snapshots according to docking ranking) as well as MD simulation (ensemble 2: which consists of 10 snapshots each of which represents binding pose which has been established during long MD run). Loading those two ensembles in pymol as 2 different models (in NMR-like model format) I need to performs some analysis to find some shared trends in each of them e.g RMSD of the distances between common residues-pairs found in contact map analysis or something else. What are most trivial suggestions might be in that particular case? Thanks for the suggestions! James |