Thank you very much, Tom. I found the folder and added a file 'chimera.pth' to system Python site-packages with the path to Chimera's site-packages, which also did the same thing. The whole point for me doing this was to try and take advantage of Chimera's functionality. I would like to slice closed 3D volumes. I've looked through the online documentation but have not had success. Could you please point me in the right direction on how to achieve this? My input will be *vertices and polygons* together with a slicing plane and my expected output is the *contents of the plane as an 'image'**or set or polygons*. Many thanks. Paul On 16/02/2016 23:52, Tom Goddard wrote:
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 F: +44 1223 49 44 68 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- 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 F: +44 1223 49 44 68