# [Chimera-users] Installing colorbrewer for Chimera Python

Tom Goddard goddard at sonic.net
Wed Feb 17 10:50:06 PST 2016

```Hi Paul,

Hi Paul,

I suggested adding the path to sys.path in your Chimera start-up so that you wouldn’t have to modify the system Python.

Here is a Python example of computing a triangulation for the part of a plane inside a closed surface, using as an example an icosahedron for the closed surface.  You can just use File / Open… in Chimera to run it and it will report in the Reply Log (menu Favorites)

Clipped icosahedron, clip plane has 10 triangles

More Python code examples are on the Chimera Python scripts web page:

http://plato.cgl.ucsf.edu/trac/chimera/wiki/Scripts

The Chimera programming documentation is scant.  To figure out how to write the attached example code I looked at my Chimera distribution at file

Chimera.app/Contents/Resources/share/SurfaceCap/surfcaps.py

at the calculate_cap() routine.  All of the Chimera Python modules are in the above “share” directory — it is useful to poke around in there to figure out how things work, although it can be hard to find what you want.

Tom

> On Feb 17, 2016, at 1:28 AM, Paul Kibet Korir <pkorir at ebi.ac.uk> wrote:
>
> 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/>https://pypi.python.org/pypi/colorbrewer/ <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 at cgl.ucsf.edu <mailto:Chimera-users at cgl.ucsf.edu>
>>> Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <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

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