[phenixbb] Nitric Oxide metal.edits not working?

Yarrow Madrona amadrona at uci.edu
Mon Mar 9 16:49:32 PDT 2015


Hello,

I am running phenix version 1.9-1692. I have restrains for a nitric oxide
ligand that I have used previously to refine a heme iron-NO linked
structure. I have pasted them below. For some reason. The NO always gets
moved a little to far from the iron. Here is a coot screen shot:

https://www.dropbox.com/s/85c1ad2kecwebij/coot.png?dl=0
Can someone please help me resolve this issue? Thank you.

-Yarrow

----------------------------------------------------------------------------------
metal edits file:

refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = name  FE  and chain A and resname FE and resseq  499
    atom_selection_2 = name  N   and chain A and resname NMO and resseq  510
    distance_ideal = 1.75
    sigma = 0.1
  }
}

refinement.geometry_restraints.edits {
  angle {
    action = *add
    atom_selection_1 = name FE  and chain A and resname FE and resseq  499
    atom_selection_2 = name N   and chain A and resname NMO  and resseq  510
    atom_selection_3 = name O   and chain A and resname  NMO  and resseq
 510
    angle_ideal = 160
    sigma = 5
  }
}

refinement.geometry_restraints.edits {
  bond {
    action = *add
    atom_selection_1 = name  FE  and chain B and resname FE and resseq  499
    atom_selection_2 = name  N   and chain B and resname NMO and resseq  510
    distance_ideal = 1.75
    sigma = 0.1
  }
}

refinement.geometry_restraints.edits {
  angle {
    action = *add
    atom_selection_1 = name FE   and chain B and resname FE and resseq  499
    atom_selection_2 = name N   and chain B and resname NMO  and resseq  510
    atom_selection_3 = name O   and chain B and resname NMO  and resseq 510
    angle_ideal = 160
    sigma = 5
  }
}
---------------------------------------------------------------------
CIF file

#
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
NMO NMO "nitric oxide             " ligand 2 2 .
#
data_comp_NMO
#
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
NMO         N       N   N     .         -0.1324   -0.0924    0.5896
NMO         O       O   O     .          0.1324    0.0924   -0.5896
#
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
NMO  N       O      double        1.223 0.020
#
loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
NMO plan-1  N      0.020
NMO plan-1  O      0.020
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