VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 29 2013 - 10:56:02 CST

Hi,
  I think that if you trim your PYTHONPATH before you start VMD,
you'll eliminate the problem. If you can't trim the path, then
installing VMD (and/or your Python libs) in a directory with a
much shorter path length would allow you to keep the same set of
directories in your PYTHONPATH, while also not overrunning whatever
limit Python has internally.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 29, 2013 at 04:56:21PM +0100, francesco oteri wrote:
> Dear vmd developers,
> I am facing a problem when running vmd in linux.
> I recently installed a python module and correctly updated the PYTHONPATH
> environment variable in my .bashrc file.A
> After this event, I got the error:
> Word too longA
> when I attempted to run vmd.A
> Looking at the code, I found that the guilty line isA
> setenv PYTHONPATH ${PYTHONPATH}:${VMDDIR}/scripts/pythonA
> in vmd script.
> The PYTHONPATH variable before running vmd is:
> /ibpc/etna/oteri/PKG/modeller/9.11/modlib:/ibpc/etna/oteri/PKG/modeller/9.11/lib/x86_64-intel8/python2.5:/ibpc/etna/oteri/PKG/networkx/1.6/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/setuptools/0.6c12/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/matplotlib/1.1.0/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/numpy/1.6.2/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/MDAnalysis/0.7.7/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/pupynere/1.0.15/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/modeller/9.11/modlib:/ibpc/etna/oteri/PKG/modeller/9.11/lib/x86_64-intel8/python2.5:/ibpc/etna/oteri/PKG/networkx/1.6/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/setuptools/0.6c12/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/matplotlib/1.1.0/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/numpy/1.6.2/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/MDAnalysis/0.7.7/lib/python2.7/site-packages:/ibpc/etna/oteri/PKG/pupynere/1.0.15/lib/python2.7/site-packages:
> Best regards,A
> Francesco 

-- 
NIH Center for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
http://www.ks.uiuc.edu/~johns/           Phone: 217-244-3349
http://www.ks.uiuc.edu/Research/vmd/       Fax: 217-244-6078