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
OK. So I've managed to 'resolve' this. Though it will not work if I install 'colorbrewer' on my system. The solution is to set a .pth file in the system site-packages folder e.g. chimera.pth with the path to Chimera site-packages (e.g. /Applications/Chimera.app/Contents/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages) That did it for me. Paul On 16/02/2016 12:08, 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 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
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 Manage subscription: http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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
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@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@cgl.ucsf.edu <mailto:Chimera-users@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
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@ebi.ac.uk <mailto:pkorir@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@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
-- 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
participants (2)
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Paul Kibet Korir -
Tom Goddard