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?
Give the chains unique chain letters?
I'm not sure if I get your question, but what I expect to have is the same PDB chain structure that was in the starting structure. Please take a look at the images below to see what I mean. Now that the the chains are not partitioned the same way as the starting model, there's no obvious way for me to superimpose the structures and calculate the RMSD.
If these are separate logical chains, they need different letters. You can't have two chain As.
If you mean to have multiple copies of one chain all of which are chain A, and have identical internal geometry - like crystal symmetry - then you need to be using the symmetry mode to duplicate one copy of A and B. If these are all in one asymmetric unit - they should be different chain letters.