[phenixbb] Restraints file for a modified peptide

Nigel Moriarty nwmoriarty at lbl.gov
Mon Aug 5 15:15:14 PDT 2013

A non-standard amino acid will be automatically linked into a chain if:

1. The atoms are with 3.0 angstom
2. The atom names of the linking atoms are consistent with the standard
names, N, CA, O, C.

To add a covalent between a the amino acid and the tag, you have choices.

A. In recent versions of phenix.refine, you can use the flag
B. You can generate some linking files using phenix.ligand_linking. This
option allows you edit the link parameters to you liking.
C (and least recommended) Have LINK records in you model and use

I'm happy to take a look at the specific residues in questions.



NB. Any files sent to me will be held in strictest confidence.

On Mon, Aug 5, 2013 at 2:36 PM, Michael Feldkamp <
michael.d.feldkamp at vanderbilt.edu> wrote:

> I have a peptide that has a fluorescent tag attached to its N-terminus
> along with a unnatural amino acid incorporated into the sequence.  I know
> how to generate .cif files for the individual ligands using elbow, but I'm
> at a loss as to get Phenix to recognize these modifications to the peptide
> so that it refines the structure as one molecule with covalent linkages
> between the fluorescent tag, peptide and modified amino acid.  Any help
> would be much appreciated.
> Thanks,
> Michael
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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