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
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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