Dear all, I am interested in carrying out PCA analysis on two trajectories- 1) protein in water and 2) protein with ligand in water. I would like to know, if there is a procedure by which we can compare the extreme1 pdbs (constituted by the movements that contribute to EV1) from both the trajectories. If yes, do we need to concatenate both the trajectories? I would be grateful if you could share some of your ideas on this matter.
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