[MMTK] Errors with PyMol visualization.

Roel Sigifredo Sanchez-Carrera rsanchez at fas.harvard.edu
Wed Oct 29 01:36:43 UTC 2008



Dear MMTK users,

We installed all the required packages in Ubuntu 7.04, and installed the
following versions of ScientificPython and MMTK:

MMTK-2.5.24
ScientificPython-2.8

We also installed the "stock" pymol of Ubuntu, version:
Pymol 0.98+0.99

We also tried a newer "binary" version of PyMol, that we could download because
Harvard is an educational institution, and then set up PYTHONPATH to point to
that directory.

In both cases we got the following error:
   if PyMOL.in_pymol:
AttributeError: 'module' object has no attribute 'in_pymol'

We tried finding this error in the mailing list, to no avail.

Pymol is launched, and then we get this error. We get it when we run any of the
tests in the Tests/ directory or when we run examples from the website because
it mostly does from MMTK import *, and therefore imports Visualization when we
get the error.

The full trace is:


aspuru at aspuru:~/Projects/MMTK/MMTK-2.5.24/Tests$ python basic_tests.py
Traceback (most recent call last):
  File "basic_tests.py", line 2, in <module>
   import MMTK
  File "/usr/lib/python2.5/site-packages/MMTK/__init__.py", line 44, in <module>
    from Universe import InfiniteUniverse, OrthorhombicPeriodicUniverse, \
  File "/usr/lib/python2.5/site-packages/MMTK/Universe.py", line 10, in <module>
    import Bonds, ChemicalObjects, Collections, Environment, \
  File "/usr/lib/python2.5/site-packages/MMTK/ChemicalObjects.py", line 8, in
<module>
    import Bonds, Collections, ConfigIO, Database, Units, Utility, Visualization
  File "/usr/lib/python2.5/site-packages/MMTK/Collections.py", line 7, in
<module>
    import ConfigIO, Utility, Units, ParticleProperties, Visualization
  File "/usr/lib/python2.5/site-packages/MMTK/Visualization.py", line 532, in
<module>
    if PyMOL.in_pymol:
AttributeError: 'module' object has no attribute 'in_pymol'
freeglut (pymol): Unable to create direct context rendering for window 'PyMOL
Viewer'
This may hurt performance.
Xlib:  extension "XFree86-DRI" missing on display ":0.0".
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python2.5/UserDict.py", line 22, in __getitem__
    raise KeyError(key)
KeyError: 'PYMOL_PATH'
Traceback (most recent call last):
  File "<string>ta", line 1, in <module>
  File "/usr/lib/python2.5/UserDict.py", line 22, in __getitem__
    raise KeyError(key)
KeyError: 'PYMOL_DATA'
Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/usr/lib/python2.5/UserDict.py", line 22, in __getitem__
    raise KeyError(key)
KeyError: 'PYMOL_PATH'

Any help will be greatly appreciated. We are under a large deadline and MMTK
will save us a LOT of time.

Many thanks!

Roel Sanchez

Harvard University




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