[phenixbb] cyclic peptide refinement

wei xia weixia1984 at outlook.com
Thu Dec 12 08:14:13 PST 2013

Hi, I am trying to refine a structure with a cyclic peptide ligand.I create a 'TRANS' link between the C-ter and N-ter residues of the cyclic peptide during refinement.But there is obvious no bond formed between the two residues in the refined structure.I checked the geo file and found that there are only angle restraints but no bond restraints between the two residuesAnyone can help me out?Thanks in advance!

refinement.pdb_interpretation.apply_cif_link {
       data_link = TRANS
       residue_selection_1 = chain D and resname MVA and resid 5005
       residue_selection_2 = chain D and resname ARG and resid 5001
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