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
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