Hi,<br><br>I am trying to refine protein structure with MCLR ligand - this is cyclic hepta-peptide which has some non-standard amino acids. Sequence is DAL-LEU-ACB-ARG-1ZN-FGA-DAM. It&#39;s exactly the same compound as chain G at 3dw8 PDB entry.<br>
<br>I could successfully import amino acids in coot through &quot;get monomer&quot; option, renumber and combine in one chain. Problem is that whenever I use phenix.refine it returns all residues nonbonded. Corresponding carboxyl and amino groups are in close proximity to make a bond. I tried to write LINKR record in .pdb - with no success:<br>
...<br>LINKR             1ZN G   5                     FGA G   6              trans<br>LINKR             FGA G   6                     DAM G   7              trans<br>...<br><br>Is there a way to create peptide bonds in this inhibitor chain? I&#39;m using phenix Version: 1.7.3.<br>
<br>Thanks in advance,<br>Vitali<br><br>