[chimerax-users] Coordset command not working in nogui mode

[Eric Pettersen]

Hi Shubham,
	Since the "coordset" command sets up playback of coordinate frames, it doesn't actually do anything until a frame is drawn, which is why in nogui mode nothing changes, and why you have to "create a delay" in GUI mode.  You can force a frame to get drawn with the "wait 1" command, which will get your script working in both modes.
	Alternatively, if you have the structure model in a variable (i.e. from the list of models returned by the 'open' command, or culled from session.models), you can change the coordset directly, e.g.:

	# if the structure model is in the 's' variable
	for cid in s.coordset_ids:
		s.active_coordset_id = cid
		# do whatever you need to do with this coordset

--Eric

	Eric Pettersen
	UCSF Computer Graphics Lab


> On May 24, 2022, at 1:22 AM, Shubham Devesh Ramgoolam via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Hi all,
> I hope you are doing well.
>  
> I have a python script for measuring the distance between aromatic rings of specific residues for different frames of a trajectory.
> To measure the distance, I am first defining centroids at the center of aromatic rings and then use the command distance. This process is repeated for each frame to be analyzed.
> To navigate between frames, I am using the command ‘coordset #1 {desired frame}’.
>  
> When executing the script in no gui mode, the centroids are always defined with respect to the residue’s location in frame 1 even though the command coordset has changed the frame.
>  
> In gui mode, the script only works if a delay is created between changing the frame and defining the new centroids.
> I introduced that delay by asking for a dummy user input (I ran the script from python Shell):
> run(session, 'coordset #1 ' + {new_frame})
> y = input('dummy')
> run (session, 'define centroid /A:8 & aromatic-ring radius 0.3 color yellow mass false name d1’)
>  
> My chimeraX version: 1.4rc202205060510 (2022-05-06)
>  
> Should I be using a different command for changing frames of trajectories when in nogui mode?
>  
> Regards,
> Shubham
>               
>  
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>  
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