Hi all,

I am working on a cryo em map of a multi domain protein. I am using alpha-fold structure model to fit in the cryo em map. However, due to conformational flexibility the whole multi-domain chain did not fit well with the map. So i took separate domains from the chain and tried fitting with the map which really worked out. But, now the domains need to be linked through peptide bond to make the full chain structure. I tried linking in coot, but as the chain IDs are different, coot couldn't do that. Pymol and chimera also didn't work out.

I would be a great help if anyone could share the correct way of linking the chains.