There are many ways you can use PyMOL for the analysis of protein-ligand interactions. It would be helpful to state what type of interactions you are particularly interested in. However, the most obvious one is to analyze hydrogen-bond formation between the complex. It is pretty well explained in the PyMOL Wiki ( http://www.pymolwiki.org/index.php/Displaying_Biochemical_Properties#Hydrogen_bonds_and_Polar_Contacts ), which is a great resource anyway. Then I would look at obvious signs of planar stacking of aromatic rings. In addition steric clashes can be analyzed quite well using the show_bumps command in PyMOL ( http://www.pymolwiki.org/index.php/Show_bumps ). Hope this helps you a little for a start.