Running_chimera_in_R
From: Bipasa Show <bipasa.show22ug@apu.edu.in> Subject: Running_chimera_in_R Date: October 21, 2024 at 10:48:18 PM PDT To: chimerax-users@cgl.ucsf.edu
Dear Team Chimera X, Hope this email finds you well. I am reaching out in order to know if there is a way I can use R to automate specific processes in Chimera and Chimera X like structure-based sequence alignment, finding SASA for multiple residues etc. . It would be nice if you could let me know if automation in these softwares are possible using R. Thanks and regards, Bipasa
Hi Bipasa, Some light Googling suggests that R can interface to Python, and both Chimera and ChimeraX's functionality are available through Python. If you are fluent enough in Python to actually get the interface between the Chimera(X) Python and R to work, you might be better served just writing your code entirely in Python. In any event, ChimeraX is probably a better choice than Chimera since ChimeraX has better programming documentation <https://www.cgl.ucsf.edu/chimerax/docs/devel/index.html> and is available as a standalone Python package <https://pypi.org/project/ChimeraX/>. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Oct 22, 2024, at 8:24 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
From: Bipasa Show <bipasa.show22ug@apu.edu.in> Subject: Running_chimera_in_R Date: October 21, 2024 at 10:48:18 PM PDT To: chimerax-users@cgl.ucsf.edu
Dear Team Chimera X, Hope this email finds you well. I am reaching out in order to know if there is a way I can use R to automate specific processes in Chimera and Chimera X like structure-based sequence alignment, finding SASA for multiple residues etc. . It would be nice if you could let me know if automation in these softwares are possible using R. Thanks and regards, Bipasa
ChimeraX-users mailing list -- chimerax-users@cgl.ucsf.edu To unsubscribe send an email to chimerax-users-leave@cgl.ucsf.edu Archives: https://mail.cgl.ucsf.edu/mailman/archives/list/chimerax-users@cgl.ucsf.edu/
Let me chime in here because I do this a lot. Since ChimeraX supports REST GET and POST commands, it is easy to remote control it from R scripts. I have attached a demo script, based on code I use in teaching. Cheers, Boris -- Boris Steipe MD, PhD Professor em. Department of Biochemistry Temerty Faculty of Medicine University of Toronto http://sentientsyllabus.org https://sentientsyllabus.substack.com
On Oct 23, 2024, at 15:52, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Hi Bipasa, Some light Googling suggests that R can interface to Python, and both Chimera and ChimeraX's functionality are available through Python. If you are fluent enough in Python to actually get the interface between the Chimera(X) Python and R to work, you might be better served just writing your code entirely in Python. In any event, ChimeraX is probably a better choice than Chimera since ChimeraX has better programming documentation and is available as a standalone Python package.
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Oct 22, 2024, at 8:24 AM, Eric Pettersen via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
From: Bipasa Show <bipasa.show22ug@apu.edu.in> Subject: Running_chimera_in_R Date: October 21, 2024 at 10:48:18 PM PDT To: chimerax-users@cgl.ucsf.edu
Dear Team Chimera X, Hope this email finds you well. I am reaching out in order to know if there is a way I can use R to automate specific processes in Chimera and Chimera X like structure-based sequence alignment, finding SASA for multiple residues etc. . It would be nice if you could let me know if automation in these softwares are possible using R. Thanks and regards, Bipasa
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participants (2)
-
Boris Steipe -
Eric Pettersen