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 Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows