In my macrocyclic peptide I have a lysine linked to glutamate via an isopeptide bond between the lysine NZ and the glutamate CD. I have this defined for Phenix refinement in a .phil file and it refines just fine. It would be nice if this could be translated to Coot so I could refine these linked residues without the two residues repelling each other. I have tried to use Jligand to make a new cif record for a LYS-GLU isopeptide bond, but it seems to have no effect on real space refinement in Coot. Maybe I'm missing something. I have the link record in the PDB header and I see the link in Coot, but the link does nothing to keep the lysine from repelling from the glutamate when I use real space refinement. Any advice would be greatly appreciated. What I have been doing instead is manually moving atoms and letting phenix refine, but I'd really love to let Coot refine too! -David
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