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]"
> <[log in to unmask]> 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
> <[log in to unmask]> http://pldserver1.biochem.queensu.ca/~rlc
--
--
Tim Gruene
Institut fuer anorganische Chemie
Tammannstr. 4
D-37077 Goettingen
GPG Key ID = A46BEE1A
|