Dear all who answered, the combination of - compiling cctbx from source - modifying the pymol startup script to source the cctbx setpaths.sh AND use cctbx.python (instead of /usr/bin/python) eventually works.
Thanks to all the responses to make this work. Tim On Wed, Jun 23, 2010 at 01:02:03PM -0400, Robert Campbell wrote: > On Wed, 23 Jun 2010 09:07:36 -0400 "Schubert, Carsten [PRDUS]" > <cschu...@its.jnj.com> wrote: > > > Tim, > > > > I'm shooting from the hip here, but I think the problem is that cctbx > > comes with its own python, which you would need to run both pymol and > > numpy under. According to Ralf it is at least not trivial to utilize the > > system python to run cctbx. So I think you need to compile/install pymol > > against cctbx.python and install it as a module under cctbx.python. > > Similar deal for numpy, which may already be available in cctbx, if not > > installation should be straightforward. > > > > These broad steps may work (again shooting from the hip...) > > -Install cctbx > > -link cctbx.python to python and make sure its first in your path (may > > be optional) > > -install numpy under cctbx.python (if not already present) > > -compile and install open.pymol against the cctbx.python, either via the > > renaming trick > > above or calling cctbx.python setup.py (build/install) > > > > Good luck, let us know how it works... > > I have no trouble running cctbx with pymol using the system python for both. > I also use Debian testing and various Ubuntu versions. To do so I > install cctbx from the sources. I have a web page with instructions for using > pymol and cctbx together at: > > http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/cctbx/ > > In short, I install cctbx using the self-extracting *source* not a > precompiled version. Go to http://cci.lbl.gov/cctbx_build/ and scroll down to > "Self-extracting cctbx sources for Unix". > > Once that installation is done, I go to where the cctbx.python script is (in > the <install>/cctbx_build/bin directory). I then make a link to that called > python: (i.e. ln -s cctbx.python python). > > Then to make sure that pymol "sees" the cctbx modules, I make sure > that the command in the startup script for pymol has just "python", not > "/usr/bin/python" in it so then it ends up running cctbx.python. (The setup > scripts for cctbx will place its directory and the *beginning* of the PATH > environment variable). > > I hope this helps, > Rob > -- > Robert L. Campbell, Ph.D. > Senior Research Associate/Adjunct Assistant Professor > Botterell Hall Rm 644 > Department of Biochemistry, Queen's University, > Kingston, ON K7L 3N6 Canada > Tel: 613-533-6821 Fax: 613-533-2497 > <robert.campb...@queensu.ca> http://pldserver1.biochem.queensu.ca/~rlc -- -- Tim Gruene Institut fuer anorganische Chemie Tammannstr. 4 D-37077 Goettingen GPG Key ID = A46BEE1A
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