Hi, I have a rather odd model situation, where I’m trying to manually create peptide bond restraints between two alternate conformers in refinement. I’m doing this using: ======= ... refinement.pdb_interpretation.apply_cif_link { data_link = TRANS residue_selection_1 = chain "A" and resid " 38 " and altid "B" residue_selection_2 = chain "A" and resid " 39 " and altid "C" } refinement.pdb_interpretation.apply_cif_link { data_link = TRANS residue_selection_1 = chain "A" and resid " 38 " and altid "B" residue_selection_2 = chain "A" and resid " 39 " and altid "D” } ... ======= However, running phenix.refine with this I get the error: ======= RuntimeError: Unused apply_cif_link: TRANS ['pdbres="MET A 38 "', 'pdbres="GLU A 39 “'] ======= Given that the alternate conformers have been removed from the labels, I assume that this can only be used to define links between residues, but not between specific conformers? Is there any way to do this? Thanks, Nick Nicholas Pearce Post-doctoral researcher Universiteit Utrecht