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

[Tom Goddard]

Hi Shubham,

  The ChimeraX programming manual has a section showing the Python functions for each ChimeraX command

	https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/core/commands/user_commands.html <https://www.cgl.ucsf.edu/chimerax/docs/devel/bundles/core/commands/user_commands.html>

Probably you already found that.

	Tom


> On Jun 30, 2022, at 9:45 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users at 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
>  
> 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>>
> <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 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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