[phenixbb] adding hydrogens to custom peptide bonds

Nigel Moriarty nwmoriarty at lbl.gov
Thu Dec 4 11:58:28 PST 2014


You have done a lot of work on this and I'd really like the files that you
have to date so I can make it easier in the future.

Regarding the hydrogens, I don't think Reduce will be able to help you. You
may have to add them using Coot and then leave the hydrogens alone.



Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov

On Thu, Dec 4, 2014 at 11:33 AM, Dale Kreitler <dkreitler at chem.wisc.edu>

> 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.
> Thanks,
> Dale
> --
> Dale Kreitler
> Gellman Lab
> UW Madison, Department of Chemistry
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> phenixbb at phenix-online.org
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