The bug you ran into is that the associations dialog wasn't handling non-polymer models correctly (some of your models had had all the protein removed, leaving just ligand).  I've just put in enough of a fix so that your session can be used.  If you get tomorrow's test build (following the "Test Builds" link off www.cgl.ucsf.edu/chimera) that will have the fix in it.

It's not yet a complete fix because it only handles the case where you open the associations dialog _after_ the protein deletion has occurred (which is okay for you).  I need to put in more work to make it handle the case where the deletion occurs after the associations dialog is open.  When that fix is done you will get an automated mail about it as I change the bug report from "open" to "internal-fix" -- and then it will be available in the next test build.

--Eric

                        Eric Pettersen

                        UCSF Computer Graphics Lab

                        pett@cgl.ucsf.edu

                        http://www.cgl.ucsf.edu