[Chimera-users] Trajectory superposition question

Elaine Meng meng at cgl.ucsf.edu
Wed Dec 12 11:15:30 PST 2018

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.

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 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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