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?