[chimerax-users] chimerax hbonds batch analysis

[Tom Goddard]

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 at 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.pdb
> select /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 true
> from the GUI  does not work either)
> 
> Best wishes,
> 
> Visvaldas
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