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@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@LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov