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 help. Jeff On Tue, Oct 23, 2012 at 9:12 AM, Patrick Loll 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

Patrick 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. Nigel On Tue, Oct 23, 2012 at 9:12 AM, Patrick Loll 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 [email protected] http://phenix-online.org/mailman/listinfo/phenixbb

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