[phenixbb] adding hydrogens to custom peptide bonds

[Nigel Moriarty]

Dale

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.

Cheers

Nigel

---
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>
wrote:

> 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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>
>
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