Despite what is mentionned by the authors, PHENIX.REFINE won't work with .cif files describing a deuterium's ID as a 'H' on on of its line.
ex of restraints .cif file:
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
D8U D8U 'deuterium(1+) ' ligand 1 0 .
#
data_comp_D8U
#
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
D8U H D D . -0.0699 -0.2447 0.0846
D8U D D D . -0.0699 -0.2447 0.0846
ex of restraints .cif file:
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
D8U D8U 'deuterium(1+) ' ligand 1 0 .
#
data_comp_D8U
#
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
D8U H D D . -0.0699 -0.2447 0.0846
***********
You will need to modify the last line in this case to make it work with PHENIX.REFINE:D8U D D D . -0.0699 -0.2447 0.0846
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