open ./doc/build/html/index.html In case that doesn't work, here are the basics: You *should* be able to run / import these file without changing your path To test, run 'python -m unittest discover' in the pymol directory. To test an individual module, run that file and it will do all the doctests. To build docs, you need Sphinx (I use v1.1.3), which is the standard python doc generator cd into doc and 'make html'. You can add docs as you like in the docstrings and in doc/source. xyzGeom is unused, but will replace xyzMath at some point