[chimera-dev] chimera import from unmodified python 2.5

Ondrej Marsalek ondrej.marsalek at uochb.cas.cz
Fri Aug 15 12:45:09 PDT 2008

hello again,

On Wed, Aug 13, 2008 at 23:17, Eric Pettersen <pett at cgl.ucsf.edu> wrote:
> Here's what works for me:
> env CHIMERA=/usr/local/chimera.dev
> LD_LIBRARY_PATH=/usr/local/chimera.dev/lib
> PYTHONPATH=/usr/local/chimera.dev/share:/usr/local/chimera.dev/lib:/usr/local/chimera.dev/lib/python2.5/site-packages
> python2.5
> You will have to adjust the above to your local installation, and may want
> to include the original values of LD_LIBRARY_PATH and PYTHONPATH if they are
> normally non-empty for you (i.e. in a similar fashion to your original
> export statements).
> At the resulting python prompt:
> from chimeraInit import init
> init([], nogui=True, script="py:/dev/null")
> The "script=" keyword arg prevents Chimera from giving you it's own command
> prompt since you are tricking it into believing that you've provided a
> script to execute (/dev/null is always an empty file).  Alternatively, you
> could have just typed "stop" at the prompt that Chimera gave you and gotten
> back to the python prompt.

thanks, that is what i wanted to achieve and it works on 32bit linux.
on a 64bit system (amd64, that is), however, i end up with the
traceback included below and without a working chimera. i think this
is a bug. i don't know much in that specific area, but it seems that
the dl module has been removed, see for example
http://bugs.python.org/issue2470 is this really a bug or is there a
problem with my setup? i run ubuntu 8.04 on both machines, python is
version 2.5.2 on the 64bit one. i can provide more information if

anyway, i have (at least in principle) a way to achieve the original
goal and i believe the above mentioned problem will eventually get

ondrej marsalek

In [3]: init([], nogui=True, script="py:/dev/null")
<type 'exceptions.ImportError'>           Traceback (most recent call last)

/home/andy/<ipython console> in <module>()

/home/andy/CHIMERA/share/chimeraInit.py in init(argv, nogui,
nomultisample, stereo, bgopacity, visual, screen, root, debug,
geometry, title, eventloop, exitonquit, nostatus, preferencesFile,
fullscreen, script, silent)
    305         if sys.platform in ['linux2', 'irix646', 'irix6-n32']:
    306                 # make C++ shared libraries work when dlopen'd
--> 307                 import dl
    308                 sys.setdlopenflags(sys.getdlopenflags() |

<type 'exceptions.ImportError'>: No module named dl

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