Warren Thanks for that. That's rather what I expected/feared.
I'd still be delighted to hear from anyone who may understand why Python isn't working straight out of the box. Best wishes Daniel On Tue, 2008-07-22 at 09:04 -0700, Warren DeLano wrote: > Daniel, > > This kind of complexity illustrates why we distribute standalone binaries for > Linux which include their own Python interpreter. In short, there is simply > too much heterogenaiety present in the 7+ years worth of deployed Linux > distribution / version / package-manager combinations for us to be able to > support any one of them individually. > > So to use PyMOL with a system-provided Python on Linux, our recommended > approach is to build from the open-source code using the distutils method > (python setup.py build install; python setup2.py install; ./pymol). > > However, in this case, it sounds like your system-provided Python may not > itself be working, so you may need to work with the Unbuntu folks to > straighten that out first. I can assure you that until "python" or > "python2.5" alone just works with no errors, there is little chance of PyMOL > building or running correctly. > > Cheers, > Warren > > -----Original Message----- > From: pymol-users-boun...@lists.sourceforge.net > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Daniel Rigden > Sent: Tuesday, July 22, 2008 8:25 AM > To: DeLano Scientific > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] python/pymol malfunction on new Ubuntu installation > > Warren > > Thanks for the quick reply. I tried what you suggested but I get the same > error. > > How can I check how the path has been configured? It seems as if there is > only one python so there shouldn't be scope for confusion; I can only find > one site.py, for example, in > > /usr/lib/python2.5/site.py > > [I'm assuming /usr/lib64/python2.5/site.py is a link] > > On the other hand, in Synaptic, I see > > python > python2.5 > python2.5-minimal > > all separately listed and installed, which I don;t really understand. > The Installed version of python is 2.5.2-0ubuntu1, while for the others it's > 2.5.2-2ubuntu4. > > Thanks again > > Daniel > > On Tue, 2008-07-22 at 07:59 -0700, DeLano Scientific wrote: > > Daniel, > > > > Any time you see the "import site failed" error from Python, you can infer > > that there is a problem with the Python interpreter being unable to access > > its required libraries. Messages after that aren't typically informative. > > > > This usually a path configuration issue, but I think it can also happen > > when there is a version mismatch betweehn the executable the libraries > > (running python 2.5 executables against 2.4 libraries or vice versa). > > > > If using the system-provided Python, you shouldn't have to set PYTHON_HOME > > since it will have been compiled in by default. Try the following in a new > > shell: > > > > export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ > > python2.5 ${PYMOL_PATH}/__init__.py > > > > Cheers, > > Warren > > -- > > DeLano Scientific LLC > > Subscriber Support Services > > mailto:supp...@delsci.com > > > > > > -----Original Message----- > > From: pymol-users-boun...@lists.sourceforge.net > > [mailto:pymol-users-boun...@lists.sourceforge.net] On Behalf Of Daniel > > Rigden > > Sent: Tuesday, July 22, 2008 7:39 AM > > To: pymol-users@lists.sourceforge.net > > Subject: [PyMOL] python/pymol malfunction on new Ubuntu installation > > > > Dear all > > > > First let me confess that my problem does not just involved pymol. > > However, it is hampering my use of pymol amongst other things and there > > must be many python experts who read this list. > > > > My problem, on a completely fresh Ubuntu 8.04 install, is that python > > can find modules when asked to import them. So > > > > export PYMOL_PATH=/var/lib/python-support/python2.5/pymol/ > > export PYTHONHOME=/usr/lib/python2.5 > > python2.5 ${PYMOL_PATH}/__init__.py > > > > gives me > > > > 'import site' failed; use -v for traceback Traceback (most recent call > > last): > > File "/var/lib/python-support/python2.5/pymol//__init__.py", line 109, in > > <module> > > import threading > > ImportError: No module named threading > > > > > > /usr/lib/python2.5 contains site.py, threading.py and all the rest. > > > > > > Can anyone help? I'd be very grateful. > > > > Daniel > > > -- > Dr Daniel John Rigden Tel:(+44) 151 795 4467 > School of Biological Sciences FAX:(+44) 151 795 4406 > Room 101, Biosciences Building > University of Liverpool > Crown St., > Liverpool L69 7ZB, U.K. > > > ------------------------------------------------------------------------- > This SF.Net email is sponsored by the Moblin Your Move Developer's challenge > Build the coolest Linux based applications with Moblin SDK & win great prizes > Grand prize is a trip for two to an Open Source event anywhere in the world > http://moblin-contest.org/redirect.php?banner_id=100&url=/ > _______________________________________________ > PyMOL-users mailing list > PyMOL-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/pymol-users > > -- Dr Daniel John Rigden Tel:(+44) 151 795 4467 School of Biological Sciences FAX:(+44) 151 795 4406 Room 101, Biosciences Building University of Liverpool Crown St., Liverpool L69 7ZB, U.K.
