[phenixbb] Nitric Oxide metal.edits not working?
Edward A. Berry
BerryE at upstate.edu
Mon Mar 9 19:17:08 PDT 2015
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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