[Chimera-users] Installing colorbrewer for Chimera Python

[Tom Goddard]

Hi Paul,

  The error means that you have two different colorbrewer Python modules and Chimera is getting the one that didn’t come with Chimera.  I see the Chimera colorbrewer.py file in

	/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages/colorbrewer.py

But I’m guessing you have the following colorbrewer module which is completely different from the Chimera one installed with your system Python

	https://pypi.python.org/pypi/colorbrewer/

In order for Chimera modules to work from the system Python it will be necessary that Chimera finds its own Python modules.  So you should put the above Chimera site-packages directory in front of Python system locations in the Python search path sys.path.  I would put this in your script that starts Chimera using the system Python, something like

import sys
sys.path.insert(0, '/Applications/Chimera.app/Contents/Resources/lib/python2.7/site-packages’)


  Tom

> On Feb 16, 2016, at 4:08 AM, Paul Kibet Korir  wrote:
> 
> Hi,
> 
> I want to use the chimera API and I've managed to configure a successful import of chimera except that I get that colorbrewer is not installed. 
> 
> >>> import chimera
> Traceback (most recent call last):
>   File "<stdin>", line 1, in <module>
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/__init__.py", line 73, in <module>
>     import palettes
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 103, in <module>
>     _initPresets()
>   File "/Applications/Chimera.app/Contents/Resources/share/chimera/palettes.py", line 95, in _initPresets
>     from colorbrewer import ColorBrewer
> ImportError: cannot import name ColorBrewer
> 
> What is the right way to go about this? (I could create a symbolic link to my system colorbrewer, but that doesn't seem clean).
> 
> -- 
> With kind regards,
> 
> Paul K Korir, PhD
> Scientific Programmer
> EMBL-EBI
> Main Building, A2-35,
> WTGC, Hinxton, Cambridge CB10 1SD
> P: +44 1223 49 44 22
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