I'm trying to refine a multimer of alpha-beta tubulin structures. I fitted the structures individually in Chimera and saved it as a single file containing all my alpha-beta tubulin monomers. The structure saved this way contain the alternating A and B chains of the different tubulin units (ABABAB). The refined structures, however, has only two chains A then followed by B. The A chain is the alpha-tubulin chains of all the tubulin units combined, and the B chain is also all the B chains combined (AB, where A = AAAA, and B= BBB).
My question is, how can I refine multiple structures like that, and maintain the chain structures in the outputted structure?