As long as you update the external source package (and all dependencies) to python 2, I have no objection. I feel that pymol is a moving target and if you need the latest and greatest tools, use them. My only concern is performance. If moving to python 2 has a performance hit, then I would be concerned.
For my compilations, I treat pymol as a separate beast - which includes
python in it's own little tree - so a new version of python is no problem.
Ezra
