For multichain modelling (ex. for a hetrodimer), Is it possible to force
the alignment program in modeller to choose particular chain for the
alignment?.
For example use only template A chain for 1st chain in the sequence and
template B chain for 2nd chain in the sequence.
If your template and target both have two chains, and the chains are of
similar length in template and target, then another way of thinking
about this is that you want Modeller to align the chain breaks (/) in
target and template. It should do this automatically, controlled by the
break_break_bonus parameter:
If your template and target are of dramatically different lengths, or
have different numbers of chains, then note that by default the
alignment is global, so won't probably won't do what you're hoping for.