[phenixbb] Nitric Oxide ligand keeps getting pushed far away from specified links in CIF
Nigel Moriarty
nwmoriarty at lbl.gov
Mon Nov 28 14:43:52 PST 2011
Yarrow
The space is a problem. Can you send me the PDB model (off-line) so I
can ensure that metal_coordinates is getting it right?
Nigel
On Mon, Nov 28, 2011 at 2:28 PM, Dale Tronrud <det102 at uoxray.uoregon.edu> wrote:
>
> I'm not sure this is your problem but I noticed that you have
> a space in the middle of "NO -HEM" where ever it occurs. I don't
> think it is supposed to.
>
> Dale Tronrud
>
> On 11/28/11 14:19, 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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--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709 Email : NWMoriarty at LBL.gov
Fax : 510-486-5909 Web : CCI.LBL.gov
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