[modeller_usage] Reordering chains in template structure

Hi!

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). [image: image.png]

*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