[phenixbb] refinement of peptide with non-standard aminocids
rwgrosse-kunstleve at lbl.gov
Sun May 13 10:39:55 PDT 2012
See this newsletter:
pages 3-5: FAQ
There are two methods to add links between atoms in Phenix. Which one
should I use?
Let us know if this doesn't fully answer your question.
On Sat, May 12, 2012 at 6:58 PM, Vitali Stanevich <stanevich at wisc.edu>wrote:
> 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
> LINKR FGA G 6 DAM G 7
> Is there a way to create peptide bonds in this inhibitor chain? I'm using
> phenix Version: 1.7.3.
> Thanks in advance,
> phenixbb mailing list
> phenixbb at phenix-online.org
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