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 ----- 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@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