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

Maxime Cuypers cuypers at ill.fr
Fri Jul 22 07:52:29 PDT 2011


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.


running phenix.elbow or phenix.refine with .cif file for D3O i am getting
the following error:
  Residues with excluded nonbonded symmetry interactions: 1
      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)

D3O D3O Unknown                   ligand 4 1 .
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
D3O   O      H1     single        1.350 0.040
D3O   O      H2     single        1.350 0.040
D3O   O      H3     single        0.947 0.010
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:
  Total number of atoms: 1165
  Number of models: 1
    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 \

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?

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