Another possibility is to open a copy of the first frame of your trajectory, hide it, and after each new coordset use the “align” command to fit the pair you care about to the hidden structure. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 30, 2022, at 9:45 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
I was able to find the python script for the command, thanks to the online documentation. I’ll try to work something out of this. Shubham
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From: Elaine Meng <mailto:meng@cgl.ucsf.edu> Sent: Wednesday, June 29, 2022 19:34 To: Shubham Devesh Ramgoolam <mailto:sdramgoolam@uwaterloo.ca> Cc: chimerax-users@cgl.ucsf.edu <mailto:chimerax-users@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>> <https://rbvi.ucsf.edu/chimerax/docs/user/commands/coordset.html#slider <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@cgl.ucsf.edu <mailto:chimerax-users@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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