> >From: "Frances Bernstein" <bernstei@fcb.pdb.bnl.gov> >Subject: cyclic structures > > I do not see any discussion of how to present a cyclic polypeptide or >polynucleotide (should one be synthesized someday) in the mmCIF dictionary. >The area that this affects in terms of representation is _entity_poly_seq. >which presents the sequence as linear. > > Frances C. Bernstein > I also do not see how the current mmCIF could handle cyclic topologies. However, the proposal I made a the week before last would handle these situations quite easily. Once you begin to explicitly list the links between the residues any topology can be described -- linear, branched, or cyclic. An example of a cyclic peptide would be (remember this is not approved mmCIF). loop_ _entity_link.entity_id _entity_link.mon_1_id _entity_link.mon_1_id _entity_link.link_typ _entity_link.primary B 1 2 peptide yes B 2 3 peptide yes B 3 4 peptide yes B 4 5 peptide yes B 5 6 peptide yes B 6 1 peptide yes This loop describes a six residue cyclic peptide. Residue 6 is linked back to 1. One could easily connect this via a disulfide bond to another polypeptide to construct something really interesting. Dale Tronrud