Hi,
I'm trying to run the align_all.py script
(http://pldserver1.biochem.queensu.ca/~rlc/work/pymol/align_all.py) in PyMol
running on Linux.
I've put the script in /opt/pymol/scripts, and in my .pymolrc file, I have the
following:
sys.path.append("/opt/pymol/scripts")
and if I print sys.path in the pymol command line, I get the following:
PyMOL>print sys.path
['', '/opt/pymol/modules',
'/opt/pymol/ext/lib/python2.5/site-packages/setuptools-0.6c7-py2.5.egg',
'/opt/pymol/ext/lib/python2.5/site-packages/simplejson-2.0.5-py2.5-linux-i686.egg',
'/opt/pymol/ext/lib/python25.zip', '/opt/pymol/ext/lib/python2.5',
'/opt/pymol/ext/lib/python2.5/plat-linux2',
'/opt/pymol/ext/lib/python2.5/lib-tk',
'/opt/pymol/ext/lib/python2.5/lib-dynload',
'/opt/pymol/ext/lib/python2.5/site-packages', '/opt/pymol/scripts']
However, if I try running the script, I get the following:
PyMOL>run align_all.py
Traceback (most recent call last):
File
"/home/vertrees/work/products/pymol/edu_build/dist/pymol/./modules/pymol/parser.py",
line 338, in parse
File "/opt/pymol/modules/pymol/parsing.py", line 455, in run_file
execfile(file,global_ns,local_ns)
IOError: [Errno 2] No such file or directory: 'align_all.py'
If I run the full path to the script it works:
PyMOL>run /opt/pymol/scripts/align_all.py
And I can then use the command.
Is there any obvious reason why it's not looking in the /opt/pymol/scripts
directory, even when this is in the sys.path?
Thanks,
Jens
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