Hi Jonathan, The system wouldn't know ChimeraX commands, but you could run ChimeraX from the system command line with startup options such as --nogui (no GUI) and input files such as ChimeraX command files (*.cxc). Command-line startup <https://rbvi.ucsf.edu/chimerax/docs/user/startup.html> ChimeraX startup options --nogui etc. <https://rbvi.ucsf.edu/chimerax/docs/user/options.html> Input file types <https://rbvi.ucsf.edu/chimerax/docs/user/commands/open.html#formats> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Sep 6, 2021, at 7:16 PM, Jonathan Choong via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi there,

Hope you are doing well. I just had a question regarding ChimeraX that I was hoping to get some clarity on. I was wondering whether it was possible to use ChimeraX commands (such as open, run, save) in the system command line without actually opening the application interface?

Thanks, hope to hear back from you.

Kind regards, Jonathan