[phenixbb] Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
Pavel Afonine
pafonine at lbl.gov
Mon Nov 28 14:32:45 PST 2011
Hi Yarrow,
phenix.refine always creates a .geo file that lists all the geometry
restraints used in refinement. Looking in this file you can always tell
which atoms is involved in which restraints, as well as ideal and actual
restraint parameter values (bond length, for example).
As a very first step I would check .geo file to make sure the restraints
are correctly set up for atoms in question.
Pavel
On 11/28/11 2:19 PM, Yarrow Madrona wrote:
> Hello,
>
> I am having some trouble refining a structure with Nitric Oxide
> coordinated to the Heme Fe. I attempted to merge two Cif files. One for
> another ligand (CNL) and one for NO (NO.cif). I have saved the merged file
> as CinNO2.cif. In the defualt refinement I type the following into the
> command line:
>
>
> Mymodel.mtz mymodel.pdb CinNO2.cif
>
> Phenix refine runs fine without any errors but pushes the NO much further
> than the 1.9 angstrom specified by the links in the cif file. I have
> pasted the contents of the cif file below. The NO, Fe links are at the end
> of the file. Thank you for any help you can provide.
>
> -Yarrow
>
>
>
> # Files merged : Tue Oct 4 10:11:22 2011
> #
> # CNL.cif
> # NO.cif
> #
> 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
> CNL CNL Unknown ligand 29 11 .
> NO NO Unknown ligand 2 2 .
> #
> data_comp_CNL
> #
> 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
> CNL C1 C CT . 55.3085 -9.1280 -43.0216
> CNL C2 C CH2 . 55.6432 -10.5699 -43.1750
> CNL C3 C CH2 . 54.6509 -11.3139 -43.9725
> CNL C4 C CH1 . 53.4902 -10.4784 -44.3504
> CNL C5 C CH2 . 53.9278 -9.3349 -45.0693
> CNL C6 C CH2 . 54.8932 -8.4964 -44.3064
> CNL C7 C CH3 . 56.3801 -8.3679 -42.3275
> CNL C8 C CT . 52.9353 -9.9244 -43.0573
> CNL C9 C CH3 . 52.3495 -11.0301 -42.2453
> CNL C10 C CH3 . 51.8314 -8.9341 -43.2982
> CNL O O O2 . 54.1049 -9.2461 -42.2221
> #
> 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
> CNL C1 C2 single 1.488 0.020
> CNL C1 C6 single 1.491 0.020
> CNL C1 C7 single 1.486 0.020
> CNL C1 O single 1.450 0.020
> CNL C2 C3 single 1.475 0.020
> CNL C3 C4 single 1.479 0.020
> CNL C4 C5 single 1.420 0.020
> CNL C4 C8 single 1.512 0.020
> CNL C5 C6 single 1.489 0.020
> CNL C8 C9 single 1.492 0.020
> CNL C8 C10 single 1.502 0.020
> CNL C8 O single 1.589 0.020
> #
> 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
> CNL C3 C2 C1 113.16 3.000
> CNL C5 C6 C1 112.56 3.000
> CNL C8 O C1 110.85 3.000
> CNL C6 C1 C2 112.60 3.000
> CNL C7 C1 C2 112.43 3.000
> CNL O C1 C2 99.48 3.000
> CNL C4 C3 C2 112.41 3.000
> CNL C5 C4 C3 110.02 3.000
> CNL C8 C4 C3 106.05 3.000
> CNL C6 C5 C4 113.20 3.000
> CNL C9 C8 C4 109.75 3.000
> CNL C10 C8 C4 111.96 3.000
> CNL O C8 C4 109.61 3.000
> CNL C8 C4 C5 104.53 3.000
> CNL C7 C1 C6 112.76 3.000
> CNL O C1 C6 106.18 3.000
> CNL O C1 C7 112.51 3.000
> CNL C10 C8 C9 106.70 3.000
> CNL O C8 C9 108.62 3.000
> CNL O C8 C10 110.10 3.000
> #
> loop_
> _chem_comp_tor.comp_id
> _chem_comp_tor.id
> _chem_comp_tor.atom_id_1
> _chem_comp_tor.atom_id_2
> _chem_comp_tor.atom_id_3
> _chem_comp_tor.atom_id_4
> _chem_comp_tor.value_angle
> _chem_comp_tor.value_angle_esd
> _chem_comp_tor.period
> CNL Var_01 C4 C8 O C1 10.40 30.0 3
> CNL Var_02 C9 C8 O C1 130.31 30.0 3
> CNL Var_03 C10 C8 O C1 -113.19 30.0 3
> #
> loop_
> _chem_comp_chir.comp_id
> _chem_comp_chir.id
> _chem_comp_chir.atom_id_centre
> _chem_comp_chir.atom_id_1
> _chem_comp_chir.atom_id_2
> _chem_comp_chir.atom_id_3
> _chem_comp_chir.volume_sign
> CNL chir_01 C1 C6 C7 O both
> CNL chir_02 C4 C3 C5 C8 both
> #
> data_comp__NO
> #
> 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
> NO N N N . -5.7690 4.3760 32.3600
> NO O O O . -4.8990 5.2460 32.3600
> #
> 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
> NO N O double 1.150 0.02
> #
> data_link_list
> loop_
> _chem_link.id
> _chem_link.comp_id_1
> _chem_link.mod_id_1
> _chem_link.group_comp_1
> _chem_link.comp_id_2
> _chem_link.mod_id_2
> _chem_link.group_comp_2
> _chem_link.name
> HEM-CYS HEM . . CYS . .
> bond_CYS-SG_=_HEM-FE
> NO -HEM HEM . . NO . .
> bond_HEM-FE_=_NO-N
> #
> data_link_HEM-CYS
> #
> loop_
> _chem_link_bond.link_id
> _chem_link_bond.atom_1_comp_id
> _chem_link_bond.atom_id_1
> _chem_link_bond.atom_2_comp_id
> _chem_link_bond.atom_id_2
> _chem_link_bond.type
> _chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
> HEM-CYS 1 FE 2 SG . 2.300000 0.020
> #
> loop_
> _chem_link_angle.link_id
> _chem_link_angle.atom_1_comp_id
> _chem_link_angle.atom_id_1
> _chem_link_angle.atom_2_comp_id
> _chem_link_angle.atom_id_2
> _chem_link_angle.atom_3_comp_id
> _chem_link_angle.atom_id_3
> _chem_link_angle.value_angle
> _chem_link_angle.value_angle_esd
> HEM-CYS 2 SG 1 FE 1 NC 109.471221 3.000
> HEM-CYS 1 FE 2 SG 2 CB 109.471221 3.000
> #
> data_link_NO -HEM
> #
> loop_
> _chem_link_bond.link_id
> _chem_link_bond.atom_1_comp_id
> _chem_link_bond.atom_id_1
> _chem_link_bond.atom_2_comp_id
> _chem_link_bond.atom_id_2
> _chem_link_bond.type
> _chem_link_bond.value_dist
> _chem_link_bond.value_dist_esd
> NO -HEM 1 N 2 FE . 1.900000 0.020
> #
> loop_
> _chem_link_angle.link_id
> _chem_link_angle.atom_1_comp_id
> _chem_link_angle.atom_id_1
> _chem_link_angle.atom_2_comp_id
> _chem_link_angle.atom_id_2
> _chem_link_angle.atom_3_comp_id
> _chem_link_angle.atom_id_3
> _chem_link_angle.value_angle
> _chem_link_angle.value_angle_esd
> NO -HEM 2 FE 1 N 1 O 140 3.000
> NO -HEM 1 N 2 FE 2 NC 103 3.000
>
>
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