Hi Eric, The ‘wait 1’ command is very helpful. Thank you so much! I have also tried the other method but it is not working for me. {Some background: My topology file was in prmtop format while my coordinate file was in dcd format. So, I opened both files in chimera and then saved the trajectory as a pdb. I am now using a combination of the pdb file and the dcd coordinate file in chimeraX.} This is what I got from the Python Shell of ChimeraX: run(session, 'open '+ r'C:\Users\Shubham\Desktop\SK_Lab\myfile.pdb') Out[3]: [<chimerax.atomic.structure.AtomicStructure at 0x2ef81670040>] run(session, 'open ' + r'C:\Users\Shubham\Desktop\mycoord.dcd' + ' structureModel #1') Out[4]: [] s = session.models s Out[6]: <chimerax.core.models.Models at 0x2efc7fece50> s.coordset_ids --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) ~\AppData\Local\Temp/ipykernel_9612/1923568490.py in <module> ----> 1 s.coordset_ids AttributeError: 'Models' object has no attribute 'coordset_ids' My goal with this is to get a way to obtain the total number of frames available for the trajectory. My chimeraX version 1.5.dev202205200152 (2022-05-20). Regards, Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Eric Pettersen<mailto:pett@cgl.ucsf.edu> Sent: Tuesday, May 24, 2022 22:15 To: Shubham Devesh Ramgoolam<mailto:sdramgoolam@uwaterloo.ca> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Coordset command not working in nogui mode Hi Shubham, Since the "coordset" command sets up playback of coordinate frames, it doesn't actually do anything until a frame is drawn, which is why in nogui mode nothing changes, and why you have to "create a delay" in GUI mode. You can force a frame to get drawn with the "wait 1" command, which will get your script working in both modes. Alternatively, if you have the structure model in a variable (i.e. from the list of models returned by the 'open' command, or culled from session.models), you can change the coordset directly, e.g.: # if the structure model is in the 's' variable for cid in s.coordset_ids: s.active_coordset_id = cid # do whatever you need to do with this coordset --Eric Eric Pettersen UCSF Computer Graphics Lab On May 24, 2022, at 1:22 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: 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 _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu<mailto:ChimeraX-users@cgl.ucsf.edu> Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users