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@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