I am using Chimera (Modeller) to model a loop, which locates at the C-termini of the original crystal structure. The structure of the target protein is a homodimer, however, I cannot model the two chains together. How can I  model the two chains together? I modeled chain A and chain B separately, the loops I modeled have different configurations.

Could you please help me resolve the problem?

Best regards,

Rui