Developing a ChimeraX bundle - accessing programmatically ChimeraX(GUI open) session
Hello,
I would like to develop a small bundle-plugin for automatically annotating residue labels in protein structures. I tried to access ChimeraX via command line when ChimeraX was running (GUI open) with an opened protein structure in order to study the structure objects hierarchy( chain ->residue ->atoms). This would help me understand it better and code accordingly. Unfortunately, I didn’t manage to do so.
Could you please suggest me a way, a page or terminal where I could read more about the internal structure of ChimeraX and if possible to programmatically access a session when it’s running in ChimeraX.
Kind regards, Stel Iliadis
Stel,
There is some ChimeraX developer info online, including a bundle tutorial and some API documentation, at https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html
The current session object can be accessed through the Shell tool (Tools -> General -> Shell).
Hope that helps,
Tony
________________________________ From: ChimeraX-users chimerax-users-bounces@cgl.ucsf.edu on behalf of Stylianos Iliadis via ChimeraX-users chimerax-users@cgl.ucsf.edu Sent: Wednesday, November 23, 2022 3:55 AM To: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: [chimerax-users] Developing a ChimeraX bundle - accessing programmatically ChimeraX(GUI open) session
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Hello,
I would like to develop a small bundle-plugin for automatically annotating residue labels in protein structures. I tried to access ChimeraX via command line when ChimeraX was running (GUI open) with an opened protein structure in order to study the structure objects hierarchy( chain ->residue ->atoms). This would help me understand it better and code accordingly. Unfortunately, I didn’t manage to do so.
Could you please suggest me a way, a page or terminal where I could read more about the internal structure of ChimeraX and if possible to programmatically access a session when it’s running in ChimeraX.
Kind regards,
Stel Iliadis
Hi Stel,
Here is an example using Python to interactively inspect atomic model data in ChimeraX
https://rbvi.github.io/chimerax-recipes/inspect/inspect.html https://rbvi.github.io/chimerax-recipes/inspect/inspect.html
And there are other examples using Python with ChimeraX on the ChimeraX Recipes web page
https://rbvi.github.io/chimerax-recipes/ https://rbvi.github.io/chimerax-recipes/
and information about the Python atomic data structures in the ChimeraX Programming Guide
https://www.cgl.ucsf.edu/chimerax/docs/devel/modules.html https://www.cgl.ucsf.edu/chimerax/docs/devel/modules.html
Tom
On Nov 23, 2022, at 2:55 AM, Stylianos Iliadis via ChimeraX-users chimerax-users@cgl.ucsf.edu wrote:
Hello,
I would like to develop a small bundle-plugin for automatically annotating residue labels in protein structures. I tried to access ChimeraX via command line when ChimeraX was running (GUI open) with an opened protein structure in order to study the structure objects hierarchy( chain ->residue ->atoms). This would help me understand it better and code accordingly. Unfortunately, I didn’t manage to do so.
Could you please suggest me a way, a page or terminal where I could read more about the internal structure of ChimeraX and if possible to programmatically access a session when it’s running in ChimeraX.
Kind regards, Stel Iliadis _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Anthony James Schaefer -
Stylianos Iliadis -
Tom Goddard