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