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
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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