[Chimera-users] Trajectory superposition question

Samo Lešnik samo.lesnik at gmail.com
Thu Dec 13 03:17:05 PST 2018

Dear Elaine,

thank you for your reply. I will then just use VMD plugins for this. I
though more elegant to do the whole procedure in Chimera, however if not
yet possible it is no problem.

Best regards,


On Wed, Dec 12, 2018 at 8:15 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> Dear Samo,
> If it is just to have a steadier view during playback with MD Movie, see
> “hold steady” option in MD Movie “Actions” menu.
> <
> http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html
> >
> However, normally this kind of processing is done with some other software
> (not Chimera) before you load the trajectory into Chimera for viewing.
> I don’t do this myself, but web-searching suggests it could be done with
> VMD plugin RMSDTT, or ptraj or cpptraj (in Ambertools).  It is a common
> step of trajectory processing, so there are probably other programs that do
> it too. A good place to look may be in the documentation of whichever
> program was used to create the trajectory in the first place.
> I hope this helps,
> Elaine
> -----
> Elaine C. Meng, Ph.D.
> UCSF Chimera(X) team
> Department of Pharmaceutical Chemistry
> University of California, San Francisco
> > On Dec 12, 2018, at 4:53 AM, Samo Lešnik <samo.lesnik at gmail.com> wrote:
> >
> > Dear Madam/Sir,
> >
> > I have a long MD trajectory (dcd files), and before performing analysis
> on it I would like to superimpose every frame to the protein from the first
> frame or the protein from the average one.
> >
> > I am not sure how can this easily be performed.
> >
> > Thank you for your answer,
> >
> > Samo Lešnik
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