Re: [phenixbb] refinement of peptide with non-standard aminocids

This may solve your problems. I used phenix.ligand_linking 3dw8.pdb in a recent version. You should read the article, however, as it will allow you to troubleshoot and obtain proof of linkage. Cheers Nigel On Sun, May 13, 2012 at 10:39 AM, Ralf Grosse-Kunstleve wrote:

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 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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