[Chimera-users] HELP: I'm wondering about how to access the surface data

Eric Pettersen pett at cgl.ucsf.edu
Wed Apr 21 14:05:11 PDT 2010

On Apr 19, 2010, at 11:07 AM, Thomas Goddard wrote:

> You cannot easily start Python and import Chimera.  There are a few  
> reasons for this.  1) An environment variable needs to be set  
> (LD_LIBRARY_PATH) so Chimera libraries can be found, 2) an  
> environment variable (PYTHONPATH) needs to be set so Python can find  
> Chimera modules, 3) Chimera requires exactly the Python binary that  
> comes with it so that the dozens of compiled modules work correctly  
> and unicode handling is done as expected.  Because of the  
> difficulties we don't support importing Chimera in an already  
> running Python -- but with work you could figure it out.

To supplement Tom's reply, therefore typically you let Chimera itself  
act as the Python interpreter.  For instance if you have a Python  
script contained in the file myscript.py, then:

	chimera --nogui myscript.py

will execute it (without bringing up the Chimera interface).  See:

Chimera Startup and Input


System Command-Line Options

for more about running Chimera in this mode.


	Eric Pettersen
	UCSF Computer Graphics Lab

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