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
<ang...@gm...> 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
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