[phenixbb] Nitric Oxide ligand keeps getting pushed far away from specified links in CIF

Dale Tronrud det102 at uoxray.uoregon.edu
Mon Nov 28 14:28:01 PST 2011


   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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