[phenixbb] hydrogen nomenclature

Nigel Moriarty nwmoriarty at lbl.gov
Tue Oct 23 09:59:17 PDT 2012


The difference is from PDB v2.3 (and earlier) and v3 naming. In
PHENIX, we are doing our best to accommodate both but moving to v3
exclusively would simplify some things. I'm not sure but I think the
PDB will accept both and saves them internally as v3.


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
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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

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