[chimerax-users] adding new trajectory format

[Anthony James Schaefer]

Radosław,

There is a tutorial for adding a new file format using a bundle: https://www.cgl.ucsf.edu/chimerax/docs/devel/tutorials/tutorial_read_format.html

To add multiple coordinate sets to an atomic model, you can use the "add_coordset​" or "`add_coordsets`" methods of the AtomicStructure to add the coordinates for different frames in the trajectory. There's more info on how to use these methods in their docstrings, but they basically take numpy arrays for atom coordinates in different frames of the trajectory. The add_coordset method adds one frame at a time with a N_atoms x 3 array, whereas add_coordsets can take a N_frames x N_atoms x 3 array. Once the trajectory is opened, users can run the ChimeraX command "coordset slider <model id>"​ to open a tool to flip through the frames.

Best,

Tony
________________________________
From: ChimeraX-users <chimerax-users-bounces at cgl.ucsf.edu> on behalf of Radosław Giziński via ChimeraX-users <chimerax-users at cgl.ucsf.edu>
Sent: Thursday, September 30, 2021 8:24 AM
To: chimerax-users at cgl.ucsf.edu <chimerax-users at cgl.ucsf.edu>
Subject: [chimerax-users] adding new trajectory format

[EXTERNAL SENDER - PROCEED CAUTIOUSLY]


Hi,

Is there a way I can add custom, multi-frame trajectory format to
ChimeraX so I can view multi frame trajectories?
Is there some manual that could guide me through the process like this?:
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/movie/movie.html

(scroll to the bottom)

Best regards,

Radosław Giziński


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