Hello, You create a command script file, which is simply a plain text file that contains a series of ChimeraX commands, then open it to execute the commands. See description of ChimeraX command files in the bottom section of this page: <https://rbvi.ucsf.edu/chimerax/docs/user/commands/usageconventions.html#cxc-...> You can also create special HTML files that you can view in the ChimeraX help viewer, with links you can click to execute commands. The "Quick Start Guide" is an example of that kind of file. See: <https://rbvi.ucsf.edu/chimerax/docs/user/tools/helpviewer.html> <https://www.rbvi.ucsf.edu/chimerax/docs/quickstart/index.html> I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco

On Aug 25, 2023, at 11:30 PM, UehkVt via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:

Hi, I am using ChimeraX on Linux OS.I think ChimeraX only has a single-line command window which isn't convenient for complex script. I want to know there are other ways to type multiple-line command and display protein structure whin ChimeraX at real time. could Jupyter notebook combine with ChimeraX? When we type command in Jupyter notebook, ChimeraX could display the result of the command.Could you tell me the method that can solve the above issue? Thanks! Sincerely!