Hi Ed,

  I don't know if more than one chain can be associated with a sequence in Multalign Viewer.  The documentation says

" A structure (even if it has multiple chains) cannot be associated with more than one sequence, but a single sequence can be associated with more than one structure."

    http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/multalignviewer/multalignviewer.html#association

That doesn't really say whether multiple chains of a single structure can associate with a sequence, only that multiple structures (different PDB models) can associate with the same sequence.  So I tried it as I'm sure you did and I was not able to make it associate more than one chain (I used groel 1grl) with the same sequence in a multiple alignment.  When I load the structure it associates chain A but not any of the other chains.  Then if I use MultAlign Viewer menu Structure / Associations... to associate chain B with the same sequence then it seems to lose the association of chain A.  At least when I select residues on the sequence, only chain B on the structure has residues selected.

  I'm forwarding this to the Chimera list since Elaine Meng or Eric Pettersen will have a better answer.

    Tom