Trajectory smoothing
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
Sent from Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 for Windows
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
Perfect! Thanks Elaine. Shubham
________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: January 3, 2023 3:57 PM To: Shubham Devesh Ramgoolam sdramgoolam@uwaterloo.ca Cc: chimerax-users@cgl.ucsf.edu 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
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 Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 for Windows
From: Elaine Mengmailto:meng@cgl.ucsf.edu Sent: Tuesday, January 3, 2023 14:57 To: Shubham Devesh Ramgoolammailto:sdramgoolam@uwaterloo.ca Cc: chimerax-users@cgl.ucsf.edumailto: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
Hi Shubham, I think your analysis is correct in that the slowdown for large trajectories would be high memory consumption, and the copying of the coordinates into a convenience array exacerbates that. It make the memory use about triple (original coordinates, convenience copy, smoothed coordinates) while the script runs. Referring back to the original coordinates instead of copying would reduce memory use to about double, at the cost of having to fetch/convert each coordinate set 5 times (for a smoothing window of 2). Nonetheless, the tradeoff could be worth it. I’ve attached a version of the smoothing script that refers to the original coordinates instead of copying, and you could try it out and see if it helps.
--Eric
Eric Pettersen UCSF Computer Graphics Lab

On May 15, 2023, at 9:35 AM, Shubham Devesh Ramgoolam via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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 mailto: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
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
Hi Eric,
Thank you for the script. Unfortunately, I cannot download it from either my mail app (.py file format is not supported) or the Pipermail website. Could you please email it to me as a text file (.txt)?
Best, Shubham ________________________________ From: Eric Pettersen pett@cgl.ucsf.edu Sent: May 15, 2023 9:39 PM To: Shubham Devesh Ramgoolam sdramgoolam@uwaterloo.ca Cc: ChimeraX Users Help chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Trajectory smoothing
Hi Shubham, I think your analysis is correct in that the slowdown for large trajectories would be high memory consumption, and the copying of the coordinates into a convenience array exacerbates that. It make the memory use about triple (original coordinates, convenience copy, smoothed coordinates) while the script runs. Referring back to the original coordinates instead of copying would reduce memory use to about double, at the cost of having to fetch/convert each coordinate set 5 times (for a smoothing window of 2). Nonetheless, the tradeoff could be worth it. I’ve attached a version of the smoothing script that refers to the original coordinates instead of copying, and you could try it out and see if it helps.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 15, 2023, at 9:35 AM, Shubham Devesh Ramgoolam via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
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 Mailhttps://go.microsoft.com/fwlink/?LinkId=550986 for Windows
From: Elaine Mengmailto:meng@cgl.ucsf.edu Sent: Tuesday, January 3, 2023 14:57 To: Shubham Devesh Ramgoolammailto:sdramgoolam@uwaterloo.ca Cc: chimerax-users@cgl.ucsf.edumailto: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.edumailto: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
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Okay, attached as a .txt, Also, I wanted to mention that if memory usage is a problem you might consider using the "step N" keyword when reading in your coordinates in order to read only every Nth frame.
--Eric
On May 15, 2023, at 6:16 PM, Shubham Devesh Ramgoolam via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hi Eric,
Thank you for the script. Unfortunately, I cannot download it from either my mail app (.py file format is not supported) or the Pipermail website. Could you please email it to me as a text file (.txt)?
Best, Shubham From: Eric Pettersen <pett@cgl.ucsf.edu mailto:pett@cgl.ucsf.edu> Sent: May 15, 2023 9:39 PM To: Shubham Devesh Ramgoolam <sdramgoolam@uwaterloo.ca mailto:sdramgoolam@uwaterloo.ca> Cc: ChimeraX Users Help <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Trajectory smoothing
Hi Shubham, I think your analysis is correct in that the slowdown for large trajectories would be high memory consumption, and the copying of the coordinates into a convenience array exacerbates that. It make the memory use about triple (original coordinates, convenience copy, smoothed coordinates) while the script runs. Referring back to the original coordinates instead of copying would reduce memory use to about double, at the cost of having to fetch/convert each coordinate set 5 times (for a smoothing window of 2). Nonetheless, the tradeoff could be worth it. I’ve attached a version of the smoothing script that refers to the original coordinates instead of copying, and you could try it out and see if it helps.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On May 15, 2023, at 9:35 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu mailto:chimerax-users@cgl.ucsf.edu> wrote:
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 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 mailto: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
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 https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
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 https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Shubham Devesh Ramgoolam