[chimerax-users] Coordset command not working in nogui mode

[Shubham Devesh Ramgoolam]

Hi all,
I hope you are doing well.

I have a python script for measuring the distance between aromatic rings of specific residues for different frames of a trajectory.
To measure the distance, I am first defining centroids at the center of aromatic rings and then use the command distance. This process is repeated for each frame to be analyzed.
To navigate between frames, I am using the command ‘coordset #1 {desired frame}’.

When executing the script in no gui mode, the centroids are always defined with respect to the residue’s location in frame 1 even though the command coordset has changed the frame.

In gui mode, the script only works if a delay is created between changing the frame and defining the new centroids.
I introduced that delay by asking for a dummy user input (I ran the script from python Shell):
run(session, 'coordset #1 ' + {new_frame})
y = input('dummy')
run (session, 'define centroid /A:8 & aromatic-ring radius 0.3 color yellow mass false name d1’)

My chimeraX version: 1.4rc202205060510 (2022-05-06)

Should I be using a different command for changing frames of trajectories when in nogui mode?

Regards,
Shubham


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