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 for Windows

From: Elaine Meng
Sent: Tuesday, January 3, 2023 14:57
To: Shubham Devesh Ramgoolam
Cc: 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