Zhen Gong, Your script is defining a function, but it doesn't call the function. Adding 'run(session)' to the bottom of your script should result in the log being cleared, etc. Also as far as I know, there is no "info" option for the log command, but the session.logger.info will work. Best, Tony On Thu, Jun 26, 2025 at 10:21 PM zg2234--- via ChimeraX-users < chimerax-users@cgl.ucsf.edu> wrote:

Dear ChimeraX team,

May I ask a basic question regarding running Python scripts in ChimeraX? I’m trying to execute a simple test script using the runscript command from the ChimeraX command window:

runscript ~/Desktop/test_print.py Here is the content of test_print.py:

def run(session, data=None): session.logger.info("✅ Successfully executed runscript_test.py!") from chimerax.core.commands import run as cxrun cxrun(session, "log clear") cxrun(session, "log info ✅ runscript_test.py is working")

However, nothing seems to happen—there is no output in the log window, and it seems the script is not being executed at all.

Ultimately, I would like to perform a coordinate transformation on a structure in ChimeraX using the equation:

r = RM * r0 where:

RM = [ 0.323, 0.9326, -0.1611], [-0.925, 0.2751, -0.2623], [-0.2003, 0.2337, 0.9515]

But I am currently stuck at the first step: getting a Python script to run properly in ChimeraX.

Any advice or suggestions would be greatly appreciated!

Best regards, Zhen Gong _______________________________________________ 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/