From:Pete Meyer <[email protected]>
To: John Ladasky <[email protected]>
Cc: "[email protected]" <[email protected]>
Sent: Wednesday, January 11, 2012 10:09 AM
Subject: Re: [PyMOL] PyMol 1.4 not running on Ubuntu Linux 11.10
Hi John,
>
>
>I don't think you need a re-install. My take on the problem is that using the
>repositories installs the pymol libraries to the system python (not sure
>offhand which that is for ubuntu 11.10). But pymol is apparently trying to
>start up with "/usr/bin/env python", which is picking up the python you've got
>installed in /usr/local.
>
>
>Short version - try edit pymol (probably /usr/bin/pymol) to hard-code the
>system python.
Hi Pete,
You were correct! I also got an off-line message from David Hall which
suggested the same problem. Thanks to you both, I have PyMol running again.
Here is a copy of my edited /usr/bin/pymol shell script, for anyone who might
need it:
==========
#!/bin/sh
# debian wrapper script for pymol
#
# Modified by John Ladasky 2012-01-11
# This modified script explicitly invokes the system python, /usr/bin/python.
# If this is not done, the system attempts to use /usr/env/python, which
# points at /usr/local/python by default (at least it does on Ubuntu Linux
# 11.10 -- other operating systems may vary).
export PYMOL_PATH=`/usr/bin/python2.7 -c "from imp import find_module; print
find_module('pymol')[1]"`
export PYMOL_DATA=/usr/share/pymol
export CHEMPY_DATA=/usr/share/chempy
/usr/bin/python2.7 -m pymol.__init__ ${1+"$@"}
==========
I just checked through my file system, and discovered that I have no less than
three installed Python 2.7 executables: one in /usr/bin, one in /usr/local/bin,
and a third one in /usr/lib/debug/usr/bin. All three executables are also
different sizes: 2.6 MB, 4.4 MB, and 3.8 MB, respectively. Wow, really? I'm
familiar with the idea of doing an "alternate install" of Python so that one
can have two revisions at once -- say, 2.6 and 2.7. But installing the same
version of Python multiple times, what could be the purpose of that? Does it
have something to do with protecting the system namespace? I know that Linux
depends on Python pretty heavily, and it could be lethal to overwrite an
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