On 06/16/2011 04:24 PM, zjxu wrote:
> (3) In pymol/trunk/pymol:
> python setup.py install --prefix=/BioSoft/pymol1.4.1_2011-6-16/
> python setup2.py install
> ./pymol
> However, when I load a pdb, the warning comes again. "pymol -rkqc
> script.py" complains again.

have you set PYTHONPATH before running setup2.py and ./pymol?

modules=/BioSoft/pymol1.4.1_2011-6-16/lib/python*/site-packages
export PYTHONPATH=$modules:$PYTHONPATH
python setup2.py install
./pymol

If you have another (global) PyMOL installation which can be found by 
python, the launcher will use that one! (this could be improved I guess).

Cheers,
   Thomas

-- 
Thomas Holder
MPI for Developmental Biology

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