[modeller_usage] multi-chains: modeled separately or jointly?

Hi List,

In multi-chain modeling, I am wondering if the alignment and modeling algorithms take into account multiple chains and their spatial locations concurrently or just simply model each chain separately and then combine the results.

Related to this, is the dope score assessment a sum of scores for chains in these cases (in which case, it's assumed the statistics are measuring two independent models), or the correlation of chains are considered in the statistical assessment?

Thank you in advance Amin Zia, Stanford Immunology