[chimera-dev] Biopython paths

[David Beck]

I want to second the use of Conrad's #2.  This has worked flawlessly for me for a range of python toolkits including homebrew.  In contrast, over the various versions of python through the last several years, #1 has almost always been problematic.

--
David A. C. Beck, Ph.D.
dacb at uw.edu
Chemical Engineering & eScience Institute
University of Washington, Seattle

On May 12, 2011, at 10:56 AM, Conrad Huang wrote:

> The problem you're encountering is due to Chimera having its own copy of 
> Python instead of using the installed system version.  (We chose to 
> bundle our own Chimera to avoid version issues, e.g., suppose you have 
> 2.6 installed and Chimera needs 2.7.)
> 
> In any case, there are a couple possible workarounds:
> 
> 1. Specify PYTHONPATH in your environment to include 
> C:\Python27\Lib\site-packages, so that Chimera picks up all the packages 
> you've installed.  This _should_ work, but there may be hidden gotchas 
> that we do not know about (yet).
> 
> 2. Install BioPython into Chimera's version of Python.  There is a 
> python.exe in the "bin" folder under the Chimera install location.  If 
> you install BioPython using that copy of Python, Chimera will be able to 
> use BioPython without you having to mess with sys.path.
> 
> Conrad
> 
> On 5/12/11 10:48 AM, Mateusz Dobrychłop wrote:
>> Hi,
>> 
>> I've got another problem, that also revolves around "paths". In my
>> extension I use BioPython libraries. Unfortunately, in every file I have
>> to determine the path to my Python installation
>> (sys.path.append("C:\Python27\Lib\site-packages"), because otherwise,
>> Chimera isn't able to import Biopython.
>> 
>> Is there any way to fix that?
>> 
>> Mateusz
>> 
>> 
>> 
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