[Chimera-users] Installing colorbrewer for Chimera Python

Thu Feb 18 01:16:07 PST 2016

Thanks, Tom. Very useful indeed.

I will go through these.

Kind regards,

Paul

On 17/02/2016 18:50, Tom Goddard wrote:
> 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 
>> <mailto: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/
>>>
>>> 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
>>>
>>
>> -- 
>> 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
>

-- 
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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