I have a template of four single chains, however in the target (single-chain) structure the chain segments are in a different order (as shown in the image).

Is it possible to somehow specify this correctly in the alignment file? Currently I reorder the chains in the PDB manually, in order to be able to specify an alignment. If I make four separate entries in the alignment file (one for each chain), then the restraints between the chains are not taken into account and my structure falls apart. 

Thank you & best regards,

Ajasja