Thank you! I thought it must be some stupid mistake. It works now. Visvaldas On Monday, November 28, 2022 at 10:19:19 PM GMT, Tom Goddard <goddard@sonic.net> wrote: The "--script" option in ChimeraX 1.4 only takes Python scripts, not ChimeraX command scripts. The clue to this is in the error message where is says it is in function "open_python_script". ChimeraX 1.5 accepts either Python or ChimeraX (.cxc) scripts with the --script option. For ChimeraX 1.4 just use chimerax --nogui myscript.cxc The --script option is mostly intended to pass arguments to a script. Tom On Nov 28, 2022, at 2:00 PM, Visvaldas K. via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote: Dear ChimeraX wizards, I was trying to generate hbond analysis via nogui, by issuing "chimerax --nogui --script "myscript.cxc", where in the script I put the following commands: open /Users/visvaldas/temp0000.pdbselect /B hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true quit However, something is wrong with hbonds line since I am getting this error:Executing: runscript myscript.cxc Traceback (most recent call last): File "/Applications/ChimeraX-1.4.app/Contents/Library/Frameworks/Python.framework/Versions/3.9/lib/python3.9/site-packages/chimerax/core/scripting.py", line 83, in open_python_script code = compile(data, stream.name, 'exec') File "myscript.cxc", line 4 hbonds sel saveFile /Users/visvaldas/temp00.hbonds restrict cross batch true ^ SyntaxError: invalid syntax What I am doing wrong? (Also, when using GUI, the hbonds line was much longer, so I deleted those reveal, color, etc entities to make it more relevant to batch. (The "long" line hbonds sel saveFile /Users/visvaldas/temp00.hbonds color #fffb00 dashes 5 restrict cross reveal true retainCurrent truefrom the GUI does not work either) Best wishes, Visvaldas _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users