As far as I understand it (not very far), the PDB version 3 format changes the naming of ribose ring atoms in nucleic acid to the conventional C1', C2' etc from the version 2 C1* etc
The dictionaries supplied with Coot & Refmac have the V2 style names C1* etc
eg a/ADP.cif
data_comp_ADP
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
ADP O2A O OP -0.500 0.000 0.000 0.000
ADP PA P P 0.000 1.026 1.100 0.106
ADP O1A O OP -0.500 1.921 1.136 1.326
ADP O3A O O2 0.000 2.021 1.042 -1.149
ADP PB P P 0.000 1.545 0.853 -2.667
ADP O3B O OP -0.660 2.802 0.361 -3.341
ADP O2B O OP -0.660 0.421 -0.149 -2.613
ADP O1B O OP -0.660 1.204 2.233 -3.157
ADP O5* O O2 0.000 0.378 2.570 0.052
ADP C5* C CH2 0.000 -0.566 2.955 -0.916
ADP H5*1 H H 0.000 -1.399 2.252 -0.844
ADP H5*2 H H 0.000 -0.084 2.847 -1.890
ADP C4* C CH1 0.000 -1.083 4.370 -0.761
ADP H4* H H 0.000 -1.632 4.428 0.189
ADP C3* C CH1 0.000 -2.090 4.668 -1.916
... etc
Should these dictionaries be changed?
Phil