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Hi I have had a play around with the Copy Chain Assignments. The Copy Chain Assignments works great if the destination chain is a mutated version of the source chain or has deleted residues (so I dont think it is a problem with the project). The Residue Mapping panel at the bottom recognises both these situations. It only seems to have a problem if the second chain has extra residues. When this is the case the Residue Mapping does not show the extra residues in the destination column and the Copy Chain Assignments fails. Dont know if this helps Cheers Ben