Hi Maxime, Try changing energy type symbol in the cif file to H instead of D. E.g " 3O H1 D H -0.294 -11.4013 -13.8002 -42.6392" I would leave the cif_link out, it should not be necessary if the D3O+ is not covalently linked to the protein... HTH, Esko On 22.7.2011, at 16.52, Maxime Cuypers wrote:
hello,
apologies if this problem has already been reported, i browsed for a while and i am running out of ideas to solve my problem. i have a neutron structure i was refining fine with phenix.refine untill i had to add a D3O water.
description:
running phenix.elbow or phenix.refine with .cif file for D3O i am getting the following error: ... Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" O D3O W 1 " occ=0.53 ... (2 atoms not shown) pdb=" D3 D3O W 1 " occ=0.53 Number of atoms with unknown nonbonded energy type symbols: 3 "HETATM 2 D1 D3O W 1 .*. D " "HETATM 3 D2 D3O W 1 .*. D " "HETATM 4 D3 D3O W 1 .*. D " Time building chain proxies: 0.01, per 1000 atoms: 2.50
Sorry: Fatal problems interpreting PDB file: Number of atoms with unknown nonbonded energy type symbols: 3 Please edit the PDB file to resolve the problems and/or supply a CIF file with matching restraint definitions, along with apply_cif_modification and apply_cif_link parameter definitions if necessary. Also note that phenix.ready_set and phenix.elbow are available for creating restraint definitions (CIF files). *******************
i then modified the .param file implementing the apply_cif_modification and apply_cif_link parameters:
refinement { main { number_of_macro_cycles = 10 ordered_solvent= false scattering_table= neutron } hydrogens { refine= individual } pdb_interpretation.apply_cif_modification { data_mod = D3O residue_selection = resname D3O } pdb_interpretation.apply_cif_link { data_link = D3O residue_selection_1 = chain W and resname D3O } } ... **************************
the .cif file i have was created with phenix.ready_set: ( i added first line after it failed without)
data_mod_D3O # 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 D3O D3O Unknown ligand 4 1 . # data_comp_D3O # 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 D3O O O O -0.475 -12.5180 -14.4044 -43.0985 D3O H1 D D -0.294 -11.4013 -13.8002 -42.6392 D3O H2 D D -0.294 -13.3333 -13.3284 -43.0933 D3O H3 D D 0.063 -12.3324 -14.5311 -44.0190 # loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd D3O O H1 single 1.350 0.040 D3O O H2 single 1.350 0.040 D3O O H3 single 0.947 0.010 # loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd D3O H2 O H1 98.14 3.000 D3O H3 O H1 103.20 1.194 D3O H3 O H2 103.22 1.252
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whatever i do i systematically get the same error:
Monomer Library directory: "/usr/local/phenix-1.7.1-743/chem_data/mon_lib" Total number of atoms: 1165 Number of models: 1 apply_cif_modification: data_mod: D3O
Sorry: Missing CIF modification: data_mod_D3O Please check for spelling errors or specify the file name with the modification as an additional argument. ********************************
the command i enter is: phenix.refine xxxx.pdb xxxx.mtz D3O.ligands.cif high_res_xxxx- neutron-long-D3O.params \ refinement.input.xray_data.labels='IMEAN,SIGIMEAN'
i looked in the online phenix.refine manual but it is not mentionning what to do in such error case. where should i put "data_mod_D3O" in the parameter file? is it the real source of the error?
Could someone help me figuring out a solution to get the restraints to work for D3O(+), please?
Maxime _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb
Esko Oksanen, PhD Post-doctoral Fellow (EMBO) Groupe Synchrotron, Institut de Biologie Structurale J.P. Ebel 41, rue Jules Horowitz F-38027 GRENOBLE Cedex 1 FRANCE tel. +33 4 38 78 95 96 mob. +33 6 84 15 14 88