Hi Eric, No, I did not. I tried it now by adding the following code at the end of the first for loop: run(session, ‘close #1.*’) It made the issue worse, the computation took longer than before. I believe it is because it takes time to close these models. (Originally, I tried fixing the issue by closing the entire session and starting a new one. However, it took too much time for chimeraX to close a session, after defining lots of geometric objects.) Is there a quicker to close these models at the end of each frame? Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Eric Pettersen<mailto:pett@cgl.ucsf.edu> Sent: Monday, June 13, 2022 20:43 To: Shubham Devesh Ramgoolam<mailto:sdramgoolam@uwaterloo.ca> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trajectory computation slowing down overtime Hi Shubham, Defining those geometric objects creates models. Are you closing those models at the end of each frame? --Eric Eric Pettersen UCSF Computer Graphics Lab On Jun 11, 2022, at 11:21 PM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> wrote: I just wanted to specify that I am using the nogui mode of chimeraX for the computation. Shubham. From: Shubham Devesh Ramgoolam Sent: June 12, 2022 1:38 AM To: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> <chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu>> Subject: Trajectory computation slowing down overtime Hi all, I hope you are doing well. I have a Python script for analyzing specific residue pairs for every frame in a trajectory. It does so, by using 2 for loops: For frame in list_frames: Set current frame to frame For pair in specific_residue_pairs: Do computation The computation involves defining geometric objects(centroids, axes, planes) and performing calculations with them(distance, angles). The issue here is that as we move further in list_frames, the computation takes longer and longer. There is a somewhat linear increase in computation time, as illustrated below: <E0E35EA38D4345BE98A480EB08BE8CEC.png> Is there a way to maintain the same computation time for every frame in the trajectory? Regards, Shubham Ramgoolam 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
