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Hi Nate, I had a very similar problem which I solved by first manually adding a link record to the pdb. e.g LINK N NH2 C 6 C ALA C 5 Then running phenix.link_edits to create a restraints file. I hope that helps, May On Nov 9 2009, Nate Nicely wrote:
Dear all,
How best to handle a C-terminally amidated peptide in phenix? I defined the atom as 'N' and the resname as 'NH2' following a structure I found that also bears a C-terminally amidated peptide. However phenix.refine seems not to be making the linkage between the amide and the preceding residue. Putting the structure into phenix.elbow returns, "No unknown residues."
Thanks,
Nate N.
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