Hi ChimeraX team, For large trajectories, the smoothing algorithm in smooth_md.py slows down considerably. I suspect it is because of this line of code: coord_sets = [s.coordset(cs_id).xyzs for cs_id in s.coordset_ids] Is there a way to retrieve the original coordinates efficiently? I was looking at the code used to load the trajectories (read_coords.py in chimerax.md_crds) and I was thinking of retrieving the original coordinates from there. However, I believe this approach would not work for DCD trajectories because the coordinates are loaded one frame at a time (from my understanding of _set_model_dcd_coordinates in read_coords.py), unlike the other trajectory formats. Shubham Sent from Mail<https://go.microsoft.com/fwlink/?LinkId=550986> for Windows From: Elaine Meng<mailto:meng@cgl.ucsf.edu> Sent: Tuesday, January 3, 2023 14:57 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 smoothing Hi Shubham, Maybe you were using the old http URL for the scripts page? Here is the current https one: <https://www.cgl.ucsf.edu/trac/chimera/wiki/Scripts> The ChimeraX trajectory-smoothing script is near the bottom. There is also one for Chimera near the middle. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 2, 2023, at 3:14 PM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi all, Does chimeraX has a command for trajectory smoothing? Based on previous similar questions, I know a script was written for trajectory smoothing in chimera/chimeraX. However, I cannot not access this script because it is not found on the server anymore.
Shubham