<div dir="ltr">Dear Elaine,<div><br></div><div>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.</div><div><br></div><div>Best regards,</div><div><br></div><div>Samo</div></div><br><div class="gmail_quote"><div dir="ltr">On Wed, Dec 12, 2018 at 8:15 PM Elaine Meng <<a href="mailto:meng@cgl.ucsf.edu">meng@cgl.ucsf.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Dear Samo,<br>
If it is just to have a steadier view during playback with MD Movie, see “hold steady” option in MD Movie “Actions” menu.<br>
<<a href="http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html" rel="noreferrer" target="_blank">http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html</a>><br>
<br>
However, normally this kind of processing is done with some other software (not Chimera) before you load the trajectory into Chimera for viewing.<br>
<br>
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.<br>
<br>
I hope this helps,<br>
Elaine<br>
-----<br>
Elaine C. Meng, Ph.D. <br>
UCSF Chimera(X) team<br>
Department of Pharmaceutical Chemistry<br>
University of California, San Francisco<br>
<br>
> On Dec 12, 2018, at 4:53 AM, Samo Lešnik <<a href="mailto:samo.lesnik@gmail.com" target="_blank">samo.lesnik@gmail.com</a>> wrote:<br>
> <br>
> Dear Madam/Sir,<br>
> <br>
> 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.<br>
> <br>
> I am not sure how can this easily be performed.<br>
> <br>
> Thank you for your answer,<br>
> <br>
> Samo Lešnik<br>
<br>
</blockquote></div>