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

[Nigel Moriarty]

Maxime

Sorry but the D1, D2, D3 atom names in the PDB are supposed to be
matched automatically to the H1, H2, H3 names in the CIF restraints
file by phenix.refine. To get going you can edit the CIF restraints
and change the H1 to D1 etc. Changing the names in the PDB from D1 to
H1 would also work, but the former seems like the preferable option.

Nigel

On Fri, Jul 22, 2011 at 7:52 AM, Maxime Cuypers <cuypers at ill.fr> 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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>
>



-- 
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov