[phenixbb] C-ter amidation of peptide

[Ralf W. Grosse-Kunstleve]

Hi Nate,

NH2 is something different in the monomer library, which phenix.refine
will pick up. Could you try with a different residue name that's
not already in the monomer library?
Use the command
  phenix.where_mon_lib_list_cif
to find the location of the monomer library. Then look in e.g.
  mon_lib/n/NH2.cif
what's there and pick a name that doesn't exist.
phenix.refine uses the presence of N-CA-C-O atoms with a double-bond
for C-O to decide "this is a peptide and I should link it."
With a different residue name, hopefully elbow will give you a
working file straight away.
Let me know if it doesn't work out; if you send me the last two residues
of the chain I'll take a closer look.

Ralf