Hi Elaine, Thank you for the reply. Coordset contains the solution to the problem. However, during the visualization process, I am also computing some geometric objects for each frame. I believe I would lose this ability if I use the coordset command. I have been using a python script for the visualization process and here’s how it works: -Select residue pairs & view sel -use a while loop and session.models[0].active_coordset_id to play the trajectory -> It would be nice to be able to fit the atoms in between frames here, just like the holdSteady option -for each loop(frame): view sel, define the geometric objects and hide them before proceeding to the next loop(frame). I am thinking of going over the script that chimeraX uses to run the ‘coordset’ command and then create my own version to fit my need. My question is: How do I locate the scripts that encode commands used by chimeraX? (I tried it on my end but I do not know in which package the command is found) Regards, Shubham Ramgoolam Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Elaine Meng<mailto:meng@cgl.ucsf.edu> Sent: Wednesday, June 29, 2022 19:34 To: Shubham Devesh Ramgoolam<mailto:sdramgoolam@uwaterloo.ca> Cc: chimerax-users@cgl.ucsf.edu<mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Aligning a trajectory to its first frame Hi Shubham, The "coordset" command for playing back trajectories and the "coordset slider" command for showing a slider interface both have a "holdSteady" option for specifying which atoms to fit between frames: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jun 29, 2022, at 12:30 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi all, I hope you are doing well. Is there a way to align all the frames of a trajectory to its first frame for the purpose of visualization? I’m trying to visualize a residue pair in a trajectory and I have done the following: select both residues; view sel; play the movie. The issue here is that the position of the pair changes (the pair rotates across the screen) with the frame. Regards, Shubham Ramgoolam