Hi Sasha,
ChimeraX is geared towards interactive use and therefore may not be the best choice for bulk numerical analysis of a trajectory.  If you want to extract a large number of atomic distances to output files, I would think you be better served using CPPTRAJ or one of the suite of gmx programs, such as gmx distance.
Nonetheless, if there is some reason that ChimeraX is crucial for this in your workflow and those other programs cannot instead be used, it might be possible to add commands to dump trajectory measurements to a file.  I assume you don't actually want to plot dozens of measurements in one plot.  At any rate, so such command exists currently.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab


On Sep 4, 2025, at 12:04 PM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Dear Elain
Thank you very much for the explanation. The daily build works perfectly.
Is there a possibility to automate the selecting/plotting cycle for a large set of atom tuples using a script?
Best regards 
Sasha


-----Original Message-----
From: Elaine Meng [mailto:meng@cgl.ucsf.edu]
Sent: Monday, September 1, 2025 23:07
To: Alexandra Zahradnikova
Cc: ChimeraX Users Help
Subject: Re: [chimerax-users] Monitor distance throughout the trajectory

Hi Sasha,
Instead of writing a distance measurement to the Log at every frame of the trajectory, I think it would be easier to use the MD plotting feature, which right away will calculate and plot the distance(s) over the whole trajectory.  Then you can save a comma-separated or tab-separated values (CSV or TSV) text file with all of the measurements.  See:
<https://www.rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider>

To summarize (more details in link above)
In the MD playback slider interface, show the context menu (right-click in the slider panel, or Ctrl-click if Mac trackpad or single-button mouse) and choose Plot.  In the main window, select the two atoms to define a distance (Ctrl-click, Shift-Ctrl-click) and then in the Distances tab of the plotting dialog, choose to plot it. You can define more than one distance if you want, which would show up as multiple lines on the same plot.

Show the context menu of the plotting window and choose "Save CSV or TSV File" -- there is also an option to save the plot as an image file.

Although 1.10 has the distance plotting, you need to get a 1.11 daily build to also have the ability to save to file.  I hope this helps,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Resource for Biocomputing, Visualization, and Informatics
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Aug 31, 2025, at 8:40 AM, Alexandra Zahradnikova via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi
I would like to record the evolution of distance between two atoms along all points of a MD trajectory into a file but I cannot find a command to keep saving/displaying the distance in the log for the whole trajectory, just for individual points (although of course the actual distance is shown in the GUI when the trajectory is played).
Thanks in advance for help.
Best regards
Sasha


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