[phenixbb] Nitric Oxide metal.edits not working?

[Edward A. Berry]

Are you sure the resname of the heme iron is FE? Usually heme Fe is one
atom of the HEM residue, like
   atom_selection_1 = name  FE  and chain A and resname HEM and resseq  499
(But if that were the problem I think phenix.refine    ^^^
would stop and tell you)

On 03/09/2015 07:49 PM, Yarrow Madrona wrote:
> 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 <http://chem_comp.id/>
> _chem_comp.three_letter_code
> _chem_comp.name <http://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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