[phenixbb] refinement of peptide with non-standard aminocids

Vitali Stanevich stanevich at wisc.edu
Sat May 12 18:58:10 PDT 2012


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's exactly the same compound as chain G at
3dw8 PDB entry.

I could successfully import amino acids in coot through "get monomer"
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:
LINKR             1ZN G   5                     FGA G   6              trans
LINKR             FGA G   6                     DAM G   7              trans

Is there a way to create peptide bonds in this inhibitor chain? I'm using
phenix Version: 1.7.3.

Thanks in advance,
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