[phenixbb] hydrogen nomenclature

Patrick Loll pat.loll at drexel.edu
Tue Oct 23 09:12:25 PDT 2012


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.



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