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:


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
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?