See this newsletter:

http://www.phenix-online.org/newsletter/CCN_2011_01.pdf

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.

Ralf


On Sat, May 12, 2012 at 6:58 PM, Vitali Stanevich <stanevich@wisc.edu> wrote:
Hi,

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,
Vitali


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