[Chimera-users] Average distance between two non-bonded atoms

[Elaine Meng]

Hi Francesco,
Sorry there is no feature to calculate the average distance over a trajectory.  You could measure the distance in every frame for the whole trajectory with MD Movie menu: Analysis... Plot... Distances, select 2 atoms and choose to plot, and then on the resulting plot window, click the "Dump Values" button to write them all to a file.  Then you would have to use some other separate method to average the values in the file.

<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/framemovie.html>
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html#plotting>

I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 24, 2022, at 7:19 AM, Francesco Pietra via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hi all
> Is it any command to measure the average distance between two non bonded atoms all over a molecular dynamics trajectory? Ideally linked to examining the trajectory with Tools ... MD/Ensemble Analysis ... MDmovie (I am using psf/dcd)
> I.e., doing the average of the distance from all frames.
> Thanks
> francesco pietra