[phenixbb] hydrogen nomenclature

Jeff Headd jjheadd at lbl.gov
Tue Oct 23 09:25:42 PDT 2012

Hi Pat,

You are right that hydrogen nomenclature can be a real problem. While the
monomer library does use the older naming convention, internally Phenix is
compatible with both. Further, the program Reduce that we use to add
hydrogens to protein and RNA/DNA uses the current RCSB standard (HB2/HB3 in
your example), so you would be best served in constructing your custom .cif
definition to match the RCSB nomenclature. This should work fine in
refinement, and will simplify your submission process with the PDB.

If you run into any trouble with this, please let me know, I am happy to


On Tue, Oct 23, 2012 at 9:12 AM, Patrick Loll <pat.loll at drexel.edu> wrote:

> Hi,
> I'm trying to sort out some monomer libraries for a high-resolution
> refinement involving non-canonical amino acids, but now I've become
> side-tracked with a hydrogen nomenclature issue that seems to affect even
> canonical amino acids. I will use the example of L-leucine to illustrate:
> In the CCP4 monomer library LEU.cif, the two hydrogens on CB are named HB1
> and HB2. However, if I look at the LEU entry on the RCSB PDB site, these
> two hydrogens are named HB2 and HB3. Looking at pdbe.org is not too
> helpful, since it lists those two hydrogens as HB2 and HB3, but includes
> alternate "PDB names" of HB1 and HB2. Similar situations pertain for other
> atoms and other residues.
> Presumably I need to stick with the nomenclature found in the monomer
> library in order for refinement to work properly; but will this come back
> to bite me later when I submit coordinates to the PDB? Any insights welcome.
> Thanks,
> Pat
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20121023/aa0ce99b/attachment.htm>

More information about the phenixbb mailing list