[phenixbb] Restraints file for a modified peptide

[Pavel Afonine]

Hi Michael,

the fourth option is too use the most general way of defining bonds 
between arbitrary atoms (custom bonds):
http://www.phenix-online.org/documentation/refinement.htm#anch354
(you can use it in GUI too).

Of course more bonds you have to define less convenient this option becomes.

Pavel

On 8/5/13 3:15 PM, Nigel Moriarty wrote:
> 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 
> intra_chain=True.
> 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 
> phenix.link_edits.
>
> I'm happy to take a look at the specific residues in questions.
>
> Cheers
>
> Nigel
>
> 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 
> <mailto: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 <http://CCI.LBL.gov>
>
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