[chimerax-users] Aligning a trajectory to its first frame

[Shubham Devesh Ramgoolam]

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 at cgl.ucsf.edu>
Sent: Wednesday, June 29, 2022 19:34
To: Shubham Devesh Ramgoolam<mailto:sdramgoolam at uwaterloo.ca>
Cc: chimerax-users at cgl.ucsf.edu<mailto:chimerax-users at 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 at 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

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