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.
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