This an example of getting some packages installed into the Chimera python environment. In my case, I was interested in using the spyder IDE within the Chimera python installation. http://packages.python.org/spyder/ First, get the setuptools (easy_install) package: $ sudo -i # export PATH=$PATH:/opt/UCSF/Chimera64-2010-08-05/bin/ # export LD_LIBRARY_PATH=/opt/UCSF/Chimera64-2010-08-05/lib # sh /home/dweber/Downloads/setuptools-0.6c11-py2.7.egg --prefix=/opt/UCSF/Chimera64-2010-08-05/ That gets 'easy_install' working with the Chimera python installation. Now for the spyder IDE. It requires PyQt4, so it's not trivial, but the following seems to build and install OK (against an Ubuntu package install for Qt4, not a custom build of Qt4 in foreign; the wget commands fetch linux-specific downloads): $ sudo -i # wget http://www.riverbankcomputing.co.uk/static/Downloads/sip4/sip-4.10.5.tar.gz # tar zxvf sip-4.10.5.tar.gz # cd sip-4.10.5 # /opt/UCSF/Chimera64-2010-08-05/bin/python2.7 configure.py # make # make install # cd .. # wget http://www.riverbankcomputing.co.uk/static/Downloads/PyQt4/PyQt-x11-gpl-4.7.... # tar zxvf PyQt-x11-gpl-4.7.4.tar.gz # cd PyQt-x11-gpl-4.7.4 # update-alternatives --config qmake #select qmake-qt4 option # /opt/UCSF/Chimera64-2010-08-05/bin/python2.7 configure.py --no-designer-plugin --qmake=/usr/bin/qmake-qt4 ...<snip>... The PyQt Python package will be installed in /opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages. PyQt is being built with generated docstrings. PyQt is being built with 'protected' redefined as 'public'. The PyQt .sip files will be installed in /opt/UCSF/Chimera64-2010-08-05/share/sip/PyQt4. pyuic4, pyrcc4 and pylupdate4 will be installed in /opt/UCSF/Chimera64-2010-08-05/bin. ...<snip>... #make #make install That should satisfy the deps for spyder. Then use easy_install to get spyder installed, like so: # /opt/UCSF/Chimera64-2010-08-05/bin/easy_install spyder Then to run spyder with a chimera-like env, the following seems to work: # export CHIMERA=/opt/UCSF/Chimera64-2010-08-05 # export LD_LIBRARY_PATH="$CHIMERA/lib/" # export TCL_LIBRARY="$CHIMERA/lib/tcl8.6" # export TCLLIBPATH="{$CHIMERA/lib}" # unset TK_LIBRARY # unset TIX_LIBRARY # export LD_PRELOAD=libotf.so # export PATH=$PATH:$CHIMERA/bin # unset PYTHONHOME # unset PYTHONPATH # $CHIMERA/bin/spyder Within the spyder interactive console, it reports running python 2.7 and I see:

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import sys sys.path ['', '/opt/UCSF/Chimera64-2010-08-05/bin', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/setuptools-0.6c11-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/spyder-1.1.4-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/pyflakes-0.4.0-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/rope-0.9.3-py2.7.egg', '/opt/UCSF/Chimera64-2010-08-05/lib/python27.zip', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/plat-linux2', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-tk', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-old', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/lib-dynload', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages', '/opt/UCSF/Chimera64-2010-08-05/lib/python2.7/site-packages/PIL']

This is not quite the right path (and maybe LD_LIBRARY_PATH etc.), but a few tweaks get it working, i.e.:

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sys.path.append('/opt/UCSF/Chimera64-2010-08-05/share') sys.path.append('/opt/UCSF/Chimera64-2010-08-05/lib') import chimera chimera.version.version 'alpha version 1.5 (build 31152) 2010-08-05 19:55:24 GMT'

This may not be a complete config/setup, but it's close. The spyder interface provides autocompletion, auto help-inspection, debug facilities, workspace, etc. If anyone finds a better way to do this, please let me know. There may be better ways to do this with virtualenv, see http://clemesha.org/blog/2009/jul/05/modern-python-hacker-tools-virtualenv-f... Best, Darren -- Darren L. Weber, Ph.D. Programmer/Analyst on Chimera Development Team Resource for Biocomputing, Visualization, and Informatics Department of Pharmaceutical Chemistry University of California, San Francisco Mission Bay Campus (MC 2240), Genentech Hall (Room N453) 600 16th Street, San Francisco, CA 94158-2517 dweber[at]cgl.ucsf.edu, 415-439-0619 (google voice) http://www.cgl.ucsf.edu/chimera/