Sorry to hear you couldn't get CE to work for you. If you have time, please
email me (personally or via the PyMOLWiki) and let me know what frustrations
you had. I'd like to make it more user friendly.
To quickly answer your question about visualizing the true-CE results use
# (1) load the CE result file
# (2) call split_states to show the other molecule
Jason Vertrees, PhD (javertre@...)