Gary, 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 split_states: # (1) load the CE result file load /path/to/ceResults.txt # (2) call split_states to show the other molecule split_states ceResults HTH, -- Jason -- Jason Vertrees, PhD (javer...@{utmb,cs.dartmouth}.edu) http://www.best.utmb.edu/ http://www.pymolwiki.org/