/usr/lib/python2.7/dist-packages/MMTK/ProteinEnvironment.py is in python-mmtk 2.7.9-1.
This file is owned by root:root, with mode 0o777.
It is a symlink to /usr/lib/python2.7/dist-packages/MMTK/../../../../share/pyshared/MMTK/ProteinEnvironment.py