[phenixbb] restraints for D3O+ give problems to run in phenix.refine

[Esko Oksanen]

   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
>
>
> **********************************
>
> 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
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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