hello,<br><br>apologies if this problem has already been reported, i browsed for a<br>while and i am running out of ideas to solve my problem. i have a<br>neutron structure i was refining fine with phenix.refine untill i had<br>
to add a D3O water.<br><br>description:<br><br>running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error:<br>...<br> Residues with excluded nonbonded symmetry interactions: 1<br> residue:<br>
pdb=" O D3O W 1 " occ=0.53<br> ... (2 atoms not shown)<br> pdb=" D3 D3O W 1 " occ=0.53<br> Number of atoms with unknown nonbonded energy type symbols: 3<br> "HETATM 2 D1 D3O W 1 .*. D "<br>
"HETATM 3 D2 D3O W 1 .*. D "<br> "HETATM 4 D3 D3O W 1 .*. D "<br> Time building chain proxies: 0.01, per 1000 atoms: 2.50<br><br>Sorry: Fatal problems interpreting PDB file:<br>
Number of atoms with unknown nonbonded energy type symbols: 3<br> Please edit the PDB file to resolve the problems and/or supply a<br> CIF file with matching restraint definitions, along with<br> apply_cif_modification and apply_cif_link parameter definitions<br>
if necessary.<br> Also note that phenix.ready_set and phenix.elbow are available<br> for creating restraint definitions (CIF files).<br>*******************<br><br>i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters:<br>
<br><br>refinement {<br> main {<br> number_of_macro_cycles = 10<br> ordered_solvent= false<br> scattering_table= neutron<br> }<br> hydrogens {<br> refine= individual<br> }<br> pdb_interpretation.apply_cif_modification {<br>
data_mod = D3O<br> residue_selection = resname D3O <br> }<br> pdb_interpretation.apply_cif_link {<br> data_link = D3O<br> residue_selection_1 = chain W and resname D3O<br> }<br>}<br>...<br>**************************<br>
<br><br>the .cif file i have was created with phenix.ready_set: <br>( i added first line after it failed without)<br><br><br>data_mod_D3O<br>#<br>data_comp_list<br>loop_<br>_<a href="http://chem_comp.id">chem_comp.id</a><br>
_chem_comp.three_letter_code<br>_<a href="http://chem_comp.name">chem_comp.name</a><br>_chem_comp.group<br>_chem_comp.number_atoms_all<br>_chem_comp.number_atoms_nh<br>_chem_comp.desc_level<br>D3O D3O Unknown ligand 4 1 . <br>
#<br>data_comp_D3O<br>#<br>loop_<br>_chem_comp_atom.comp_id<br>_chem_comp_atom.atom_id<br>_chem_comp_atom.type_symbol<br>_chem_comp_atom.type_energy<br>_chem_comp_atom.partial_charge<br>_chem_comp_atom.x<br>_chem_comp_atom.y<br>
_chem_comp_atom.z<br>D3O O O O -0.475 -12.5180 -14.4044 -43.0985<br>D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392<br>D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933<br>
D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190<br>#<br>loop_<br>_chem_comp_bond.comp_id<br>_chem_comp_bond.atom_id_1<br>_chem_comp_bond.atom_id_2<br>_chem_comp_bond.type<br>_chem_comp_bond.value_dist<br>
_chem_comp_bond.value_dist_esd<br>D3O O H1 single 1.350 0.040<br>D3O O H2 single 1.350 0.040<br>D3O O H3 single 0.947 0.010<br>#<br>loop_<br>_chem_comp_angle.comp_id<br>
_chem_comp_angle.atom_id_1<br>_chem_comp_angle.atom_id_2<br>_chem_comp_angle.atom_id_3<br>_chem_comp_angle.value_angle<br>_chem_comp_angle.value_angle_esd<br>D3O H2 O H1 98.14 3.000<br>D3O H3 O H1 103.20 1.194<br>
D3O H3 O H2 103.22 1.252<br><br><br>**********************************<br><br>whatever i do i systematically get the same error:<br><br> Monomer Library directory:<br> "/usr/local/phenix-1.7.1-743/chem_data/mon_lib"<br>
Total number of atoms: 1165<br> Number of models: 1<br> apply_cif_modification:<br> data_mod: D3O<br><br>Sorry: Missing CIF modification: data_mod_D3O<br> Please check for spelling errors or specify the file name<br>
with the modification as an additional argument.<br>********************************<br> <br>the command i enter is:<br>phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx-neutron-long-D3O.params \<br>refinement.input.xray_data.labels='IMEAN,SIGIMEAN'<br>
<br><br>i looked in the online phenix.refine manual but it is not mentionning what to do in such<br>error case.<br>where should i put "data_mod_D3O" in the parameter file? is it the<br>real source of the error?<br>
<br>Could someone help me figuring out a solution to get the restraints to<br>work for D3O(+), please?<br><br>Maxime<br>