Yup, we compiled Python with the default options which uses UCS-2 instead of UCS-4. Since both Ubuntu and RedHat/Fedora use UCS-4, I'll change our Python to be the same. Tomorrow's daily build will use the UCS-4 API. FYI, while chimera can work with a stock python, it is not completely compatible. We use a newer version of Tk than the stock python, so we had to modify the Tkinter module. We also made several other patches to the Python library, e.g., the help() function so it would work better with compiled modules. What this means is that if you are going to use the stock python with chimera, you have to have extra setup code to use the chimera GUI. If you have Python code that you want to use with chimera, it's simplier to set the CHIMERAPATH environment to include the stock python's site-packages directory and your PYTHONPATH directories, or alter sys.path in your Python code. "chimera --nogui script.py" is a powerful way to run arbitrary Python code with the chimera modules. And yes, please share how you are using chimera with the stock python. It should be as "simple" as (1) setting the CHIMERA environment variable, (2) adding CHIMERA/lib to LD_LIBRARY_PATH, (3) optionally setting up Tcl and Tk to be chimera's version, (4) adding CHIMERA/share to sys.path, (3) importing chimeraInit, and (5) calling chimeraInit.init with either nogui=True or eventloop=False. Greg Couch UCSF Computer Graphics Lab On Wed, 6 Aug 2008, Ondrej Marsalek wrote:
hello everyone,
first of all, i would like to say thank you for using vanilla python 2.5, i think this could be quite useful.
unfortunately, there is one problem that keeps me from using chimera from a session of my regular python 2.5 installation (on ubuntu 8.04). after setting paths properly, an attempt to import chimera (or the binary module _chimera) produces the following exception:
In [1]: import chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last)
/home/andy/<ipython console> in <module>()
/home/andy/CHIMERA/share/chimera/__init__.py in <module>()
<type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String
In [2]: import _chimera --------------------------------------------------------------------------- <type 'exceptions.ImportError'> Traceback (most recent call last)
/home/andy/<ipython console> in <module>()
<type 'exceptions.ImportError'>: /opt/chimera/lib/libwrappy2.so: undefined symbol: PyUnicodeUCS2_AsUTF8String
it seems that the python 2.5 provided with chimera is compiled with different unicode settings than the one in ubuntu. the shared chimera objects are compiled against that version of python and therefore can't be used from my normal python. the only way i see around this at the moment is to recompile chimera, but i wanted to leave that as the very last option.
i would appreciate any suggestions, as a straightforward way to use chimera from my normal python would be really neat. i'll be glad to provide details if anyone is interested.
regards, ondrej marsalek _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu http://www.cgl.ucsf.edu/mailman/listinfo/chimera-dev