[phenixbb] adding hydrogens to custom peptide bonds

Dale Kreitler dkreitler at chem.wisc.edu
Thu Dec 4 11:33:54 PST 2014

Hi All,

I am trying to add riding hydrogens to a model that includes
beta-3-homoglutamine (B3Q). The monomer is not in the ccp4 library but it
is a PDB chemical component. So far I have used elbow to build and optimize
my own version of the ligand using the atom naming convention for a
beta-amino acid in the PDB (where CB is in the backbone adjacent to the
amino group, so the backbone goes like C-CA-CB-N). I am using a TRANS cif
link from the monomer library for the N(alpha-amino acid) to C(beta-amino
acid), and I have defined my own cif link for the N(beta-amino acid) to
C(alpha-amino acid). However when I run phenix.reduce I can't get hydrogens
to appear on the peptide bonds between the beta-amino acid and adjacent
alpha-amino acids (hydrogens appear every where else on the ligand and in
the model).

I realize the effect of two hydrogens on the model is inconsequential but I
would like to figure out how I can get phenix.reduce to recognize the bonds
to my "ligand" as standard peptide bonds and add hydrogens accordingly.


Dale Kreitler
Gellman Lab
UW Madison, Department of Chemistry
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