Pymol Doesn't Initialize after Upgrading to Python 2.6

[Timothy Palpant]

While the last rebuild updated Pymol's python dependency to include 2.6, it crashes with the following error:

Error: unable to initalize the pymol.cmd module
Traceback (most recent call last):
  File "/var/lib/python-support/python2.6/pymol/cmd.py", line 265, in <module>
    from api import *
  File "/var/lib/python-support/python2.6/pymol/api.py", line 381
     as = show_as
      ^
 SyntaxError: invalid syntax

It looks like this problem is already known; by examining the source of api.py I found this:

# dang! Python 2.6 will break PyMOL's "as" method.
# Proposal:
# 1. stick with Python <=2.5 for as long as possible
# 2. convert API method to cmd.show_as() and leave "as" in the scripting langauge
# 3. allow "show_as" in the scripting language
as = show_as

While I'm not sure exactly what's going on (never touched Python), commenting out the final line seems to correct the problem--or at least allow Pymol to start.

[Morten Kjeldgaard (mok0)]

I'd like an FFe for this upload.

I get the following error message when attempting to install the current jaunty pymol_1.1-1ubuntu1:

Processing triggers for python-support ...
Compiling /var/lib/python-support/python2.6/chempy/fast/__init__.py ...
SyntaxError: ('invalid syntax', ('/var/lib/python-support/python2.6/chempy/fast/__init__.py', 67, 23, ' ll = as[attrib]\n'))

Compiling /var/lib/python-support/python2.6/pymol/api.py ...
SyntaxError: ('invalid syntax', ('/var/lib/python-support/python2.6/pymol/api.py', 381, 2, 'as = show_as\n'))

Attached patch contains a fix.

[Martin Pitt (pitti)]

I unsubscribed ubuntu-release, there's no FF to approve here (it's just a bug fix). I subscribed ubuntu-universe-sponsors for getting it uploaded.

[Scott Kitterman (kitterman)]

ack from motu-release.

[Launchpad Janitor (janitor)]

This bug was fixed in the package pymol - 1.1-1ubuntu2

---------------
pymol (1.1-1ubuntu2) jaunty; urgency=low

  * Fix complaints when installing, "as" can no longer be used
    as a variable name (LP: #340085). The consequence is that
    the "as" keyword has become "show_as" (changed as proposed
    by upstream).

 -- Morten Kjeldgaard <email address hidden> Wed, 15 Apr 2009 14:24:39 +0200

[Gergely Katona (gkatona)]

I am still having problem with python2.6 in jaunty after the fix. The toolbar does not show up with the following error message.

 OpenGL graphics engine:
  GL_VENDOR: NVIDIA Corporation
  GL_RENDERER: Quadro FX 3450/4000 SDI/PCI/SSE2
  GL_VERSION: 2.1.2 NVIDIA 180.44
Traceback (most recent call last):
  File "/var/lib/python-support/python2.6/pymol/__init__.py", line 400, in launch_gui
    __import__(self.invocation.options.gui)
  File "/var/lib/python-support/python2.6/pmg_tk/__init__.py", line 22, in <module>
    from PMGApp import *
  File "/var/lib/python-support/python2.6/pmg_tk/PMGApp.py", line 31, in <module>
    import Pmw
ImportError: No module named Pmw
 Adapting to Quadro hardware.Setting-Error: type read mismatch (float) -1

 Detected 2 CPU cores. Enabled multithreaded rendering.

 Changing to python2.5 in the pymol wrapper script partly solves the problem, the toolbar is back however a new error " Setting-Error: type read mismatch (float) -1 " shows up repeatedly. On the other hand pymol can load and display molecules, but there might be other adverse effects upon switching back to python2.5.

[Scott Kitterman (kitterman)]

please file a new bug for this. We'll need to figure it out in a
post-release update.