[modeller_usage] Modelling with ligands while maintaining correct chain ID

Hello,

I have a template that has the following structure:

Chain A Chain B ligand 1 A ligand 2 A ligand 3 B ligand 4 B

I edit my ali file to place 4 dots at the end of the second chain before the *. This results however, in having all four ligands as part of of the B chain in my model.

How can I fix that?

Regards.