[phenixbb] refinement of peptide with non-standard aminocids

Ralf Grosse-Kunstleve rwgrosse-kunstleve at lbl.gov
Sun May 13 10:39:55 PDT 2012


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 at 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
>
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20120513/45e1fadd/attachment.htm>


More information about the phenixbb mailing list