PyMOL is one of the best protein working tools available. There are many useful scripts available and it is extremely powerful, when used correctly. The built-in Python shell makes it essentially a real-time programming environment. The user support is a class of its own. Even more so when compared to e.g. the AutoDock support, which is essentially not existing. This is even more regrettable, since some of AutoDocks features are really unique.
One internal characteristics I would like to know more details about is, what the three labels Rank, ID and Index exactly mean and how they are related to the information contained in a PDB file. Work in progress.