Hi Terry,
phenix.ready_set uses Reduce to add hydrogens to the model, which
conforms to the PDB v3.x naming convention. HB2 and HB3 ar the correct
name for these hydrogen atoms, but you're right that the
chem_data/mon_lib entry does not agree with this. We are going to
correct the PTR entry and move it to chem_data/geostd to properly
match the PDB naming convention.
Thanks for pointing out this inconsistency.
Jeff
On Mon, Nov 14, 2011 at 3:01 PM, Terry Lang
Hey Everyone,
I have found a small issue with atom naming for residue PTR. When phenix.ready_set adds hydrogens to the residue, it names the hydrogens connected to the CB atom to be HB3 and HB2. However, the hydrogens in the cif file located in chem_data/mon_lib are labeled HB1 and HB2. Manually changing either the cif file or the atom name in the pdb file solves the problem.
Terry
-- P. Therese Lang Post Doc Alber Lab, UC Berkeley
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