Hi Angelo, instead of calculating RMSD you could monitor pairwise helix angles over states. See attached script, it depends on the http://www.pymolwiki.org/index.php/AngleBetweenHelices script.
Cheers, Thomas On Thu, Mar 10, 2011 at 12:05 AM, Angelo Rossi <angelo.raymond.ro...@gmail.com> wrote: > Hello: > > I have a protein with several helices and believe only one of them (the one > closest to that active center) moves significantly during a simulation. > > Can someone suggest a way to use pymol to highlight the movement of the > helices in this protein. I want to select 20 structures from a trajectory, > highlight each helix in the protein and hopefully it will show significant > movement of this specific responsible for activity. > > Thank you for any help you can provide. > > Kind regards, > > Angelo
monitorhelices.py
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