Lion comes with Python 2.7.1 out of the box. Good choice. At last 2.5 is gone.
The Fink install of Pymol 1.5 comes with it’s own version of Python (2.7.3).
In order to invoke Pymol from Python, for running scripts with serious number crunching, you need to run the script in this version of Python – otherwise the Pymol module is naturally absent. Having MacPymol 0.99rc6 doesn’t help! There might be a way to include the Pymol module in the native Python install, but that’s above my pay scale.
/sw/bin should be in your $PATH.
If not resorting to an alias, you need to invoke python2.7