Dear Chimera Users! For my particular analysis I have 2 homologue membrane proteins (one is bacterial, and another one- mammalian cytocrome-C oxydase) each bound to same smaller (ligand) protein called for simplicity "the_guy". For that particular case the conservation in sequence of both protein is quite low however 1) the overall fold of both proteins especially within the membrane-embedded region as well as 2) ligand-bound (which is mostly the water exposed loops) region are quite similar. Now using some Chimera tool I need to estimate binding interfaces of two homologous proteins in terms of the conservation of the resides involved in binding of the_guy. Then I need to make more complex task- performing the same evolutional analysis but comparing 2 ensembles extracted from the MD trajectory represent simulation of binding of each of the protein with the_guy to track correlations of the statistics between the residues involved in the binding during MD as well as overall conservation for particular fold. Does the "Evolutionary tracing" might be useful here? Thanks for help! Gleb