Re: [phenixbb] C-ter amidation of peptide

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