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 [EXTERNAL SENDER - PROCEED CAUTIOUSLY] 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)
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Anthony James Schaefer -
Stylianos Iliadis -
Tom Goddard