[Chimera-users] python script running OUTSIDE chimera possible?

Greg Couch gregc at cgl.ucsf.edu
Thu Apr 18 14:16:31 PDT 2013

Hello Fred,

In some cases, it is possible to do what you want, but in general it is 
not possible because Chimera has its own versions of system libraries 
that it needs to work correctly -- so it depends on how different 
Chimera's version of the libraries are from the system ones, and that 
changes from release to release of Chimera and which system Chimera is 
installed on.

So you are much better off using 'chimera --nogui --silent --script 
...',  or starting up chimera and opening the .py file.

In the Chimera Programmer's FAQ, 
there is a section on how to pass arguments to scripts that shows how to 
encapsulate 'chimera --nogui --silent --script' in a Linux/Mac OS X 
shell script.    I will add a section to the Programmer's FAQ about how 
to install other Python packages into chimera.

And if you still would still like the gory details, look at the chimera 
startup script and how it manipulates environment variables.  There is 
some additional (some redundant) environment manipulation in 
CHIMERA/share/__main__.py, and then, unlike __main__.py, you would call 
chimeraInit.init([], eventloop=False) before invoking any chimera packages.



On 04/17/2013 04:08 PM, frederick lee wrote:
> hello chimera experts,
> as far as i know, python scripting for chimera is done within
> the context of chimera like
> chimera --nogui myscript.py parameters ...
> is it possible to run myscript.py without the need of the
> chimera executable and use import statements of some sort to
> access the chimera module(s) like
> python myscript.py parameters
> best regards,
> fred

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