Dear Jon,

Thank you so much for all your effort! I really appreciate it. I’ve just tried 
to load the files, but unfortunately, it still won’t open and continues to show 
the error message I’ve attached here.

Thanks again for your help.

Best regards,
Martin

From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Jon Cooper 
<0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>
Date: Monday, August 19, 2024 at 14:24
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: Re: [ccp4bb] CIF file Cannot Open by Coot
⚠ Caution: External sender


I made your cif into a pdb (attached) which looks OK. Maybe worth trying with 
that.

Best wishes, Jon Cooper.
jon.b.coo...@protonmail.com

Sent from Proton Mail Android


-------- Original Message --------
On 19/08/2024 12:42, Martin Hu <wenhao.hu...@ucl.ac.uk> wrote:

>  Dear All,
>
>  Thank you all for your help. I’ve tried several approaches to input this 
> file, including changing the format to mmCIF, importing it as coordinates, 
> and checking the restraints in the file. However, I am still unable to 
> install the experimental ligand structure into the protein. It seems that 
> COOT or JLigand cannot read the restraints from the CIF file.
>
>  I’m wondering if anyone has faced a similar problem before, and if there is 
> a way to input the experimental structure and save its restraints so that it 
> can be refined with the overall protein structure in Refmac?
>
>  I’ve attached the original CIF file here for your reference (in .txt format).
>
>  Sincerely,
>  Martin
>
>  ########################################################################
>
>  To unsubscribe from the CCP4BB list, click the following link:
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>  terms & conditions are available at 
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>  #######################################################################
>  #
>  # This file contains crystal structure data downloaded from the
>  # Cambridge Structural Database (CSD) hosted by the Cambridge
>  # Crystallographic Data Centre (CCDC).
>  #
>  # Full information about CCDC data access policies and citation
>  # guidelines are available at 
> https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.ccdc.cam.ac.uk%2Faccess%2FV1&data=05%7C02%7Cwenhao.hu.23%40UCL.AC.UK%7C4b5437b17d4c4905bbd908dcc05229e7%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C638596706623572595%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=1UNcBtGEJl2mElc8AyyDvIzhkmQzINthVoWLdUFtKPk%3D&reserved=0<http://www.ccdc.cam.ac.uk/access/V1>
>  #
>  # Audit and citation data items may have been added by the CCDC.
>  # Please retain this information to preserve the provenance of
>  # this file and to allow appropriate attribution of the data.
>  #
>  #######################################################################
>
>  data_twin5
>  _audit_block_doi                 10.5517/ccryflp
>  _database_code_depnum_ccdc_archive 'CCDC 713483'
>  loop_
>  _citation_id
>  _citation_doi
>  _citation_year
>  1 10.1016/j.dyepig.2009.03.001 2009
>  _audit_update_record
>  ;
>  2008-12-13 deposited with the CCDC.  2024-08-19 downloaded from the CCDC.
>  ;
>
>
>
>  _audit_creation_method           SHELXL-97
>
>  _chemical_name_systematic
>  ;
>
>  ?
>
>  ;
>
>  _chemical_name_common            ?
>
>  _chemical_melting_point          ?
>
>  _chemical_formula_moiety         'C9 H7 B F2 N2'
>
>  _chemical_formula_sum            'C9 H7 B F2 N2'
>
>  _chemical_formula_weight         191.98
>
>
>
>  loop_
>
>  _atom_type_symbol
>
>  _atom_type_description
>
>  _atom_type_scat_dispersion_real
>
>  _atom_type_scat_dispersion_imag
>
>  _atom_type_scat_source
>
>
>
>
>
>
>
>
>
>
>  C C 0.0033 0.0016 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
>  H H 0.0000 0.0000 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
>  B B 0.0013 0.0007 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
>  N N 0.0061 0.0033 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
>  F F 0.0171 0.0103 'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
>
>
>
>  _symmetry_cell_setting           Monoclinic
>
>  _symmetry_space_group_name_H-M   C2/c
>  _symmetry_space_group_name_Hall  '-C 2yc'
>
>
>
>  loop_
>
>  _symmetry_equiv_pos_as_xyz
>
>
>
>
>
>
>
>
>  'x, y, z'
>  '-x, y, -z+1/2'
>  'x+1/2, y+1/2, z'
>  '-x+1/2, y+1/2, -z+1/2'
>  '-x, -y, -z'
>  'x, -y, z-1/2'
>  '-x+1/2, -y+1/2, -z'
>  'x+1/2, -y+1/2, z-1/2'
>
>
>
>  _cell_length_a                   10.126(4)
>
>  _cell_length_b                   10.196(4)
>
>  _cell_length_c                   17.143(6)
>
>  _cell_angle_alpha                90.00
>
>  _cell_angle_beta                 102.285(6)
>
>  _cell_angle_gamma                90.00
>
>  _cell_volume                     1729.5(11)
>
>  _cell_formula_units_Z            8
>
>  _cell_measurement_temperature    296(2)
>
>  _cell_measurement_reflns_used    32
>
>  _cell_measurement_theta_min      2.45
>
>  _cell_measurement_theta_max      12.33
>
>
>
>  _exptl_crystal_description       plate
>
>  _exptl_crystal_colour            orange
>
>  _exptl_crystal_size_max          0.20
>
>  _exptl_crystal_size_mid          0.20
>
>  _exptl_crystal_size_min          0.04
>
>  _exptl_crystal_density_meas      'not measured'
>
>  _exptl_crystal_density_diffrn    1.475
>
>  _exptl_crystal_density_method    'not measured'
>
>  _exptl_crystal_F_000             784
>
>  _exptl_absorpt_coefficient_mu    0.119
>
>  _exptl_absorpt_correction_type   multi-scan
>
>  _exptl_absorpt_correction_T_min  0.9766
>
>  _exptl_absorpt_correction_T_max  0.9953
>
>  _exptl_absorpt_process_details   twinabs
>
>
>
>  _exptl_special_details
>  ;
>
>  ?
>
>  ;
>
>
>
>  _diffrn_ambient_temperature      296(2)
>
>  _diffrn_radiation_wavelength     0.71073
>
>  _diffrn_radiation_type           MoK\a
>
>  _diffrn_radiation_source         'fine-focus sealed tube'
>
>  _diffrn_radiation_monochromator  graphite
>
>  _diffrn_measurement_device_type  'CCD area detector'
>
>  _diffrn_measurement_method       'phi and omega scans'
>
>  _diffrn_detector_area_resol_mean ?
>
>  _diffrn_standards_number         ?
>
>  _diffrn_standards_interval_count ?
>
>  _diffrn_standards_interval_time  ?
>
>  _diffrn_standards_decay_%        ?
>
>  _diffrn_reflns_number            3845
>
>  _diffrn_reflns_av_R_equivalents  0.0000
>
>  _diffrn_reflns_av_sigmaI/netI    0.2541
>
>  _diffrn_reflns_limit_h_min       -11
>
>  _diffrn_reflns_limit_h_max       11
>
>  _diffrn_reflns_limit_k_min       -11
>
>  _diffrn_reflns_limit_k_max       11
>
>  _diffrn_reflns_limit_l_min       -19
>
>  _diffrn_reflns_limit_l_max       20
>
>  _diffrn_reflns_theta_min         2.43
>
>  _diffrn_reflns_theta_max         24.77
>
>  _reflns_number_total             3845
>
>  _reflns_number_gt                1360
>
>  _reflns_threshold_expression     >2sigma(I)
>
>
>
>  _computing_data_collection       'Bruker APEX II'
>
>  _computing_cell_refinement       'Bruker APEX II'
>
>  _computing_data_reduction        'Bruker APEX II'
>
>  _computing_structure_solution    'SHELXS-97 (Sheldrick, 1990)'
>
>  _computing_structure_refinement  'SHELXL-97 (Sheldrick, 1997)'
>
>  _computing_molecular_graphics    'Bruker SHELXTL'
>
>  _computing_publication_material  'Bruker SHELXTL'
>
>
>
>  _refine_special_details
>  ;
>
>  Refinement of F^2^ against ALL reflections. The weighted R-factor wR and
>
>  goodness of fit S are based on F^2^, conventional R-factors R are based
>
>  on F, with F set to zero for negative F^2^. The threshold expression of
>
>  F^2^ > 2sigma(F^2^) is used only for calculating R-factors(gt) etc. and is
>
>  not relevant to the choice of reflections for refinement. R-factors based
>
>  on F^2^ are statistically about twice as large as those based on F, and R-
>
>  factors based on ALL data will be even larger.
>
>  ;
>
>
>
>  _refine_ls_structure_factor_coef Fsqd
>
>  _refine_ls_matrix_type           full
>
>  _refine_ls_weighting_scheme      calc
>
>  _refine_ls_weighting_details
>  'calc w=1/[\s^2^(Fo^2^)+(0.1025P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3'
>
>  _atom_sites_solution_primary     direct
>
>  _atom_sites_solution_secondary   difmap
>
>  _atom_sites_solution_hydrogens   geom
>
>  _refine_ls_hydrogen_treatment    refall
>
>  _refine_ls_extinction_method     SHELXL
>
>  _refine_ls_extinction_coef       0.0053(16)
>
>  _refine_ls_extinction_expression Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^
>
>  _refine_ls_number_reflns         3845
>
>  _refine_ls_number_parameters     129
>
>  _refine_ls_number_restraints     0
>
>  _refine_ls_R_factor_all          0.2818
>
>  _refine_ls_R_factor_gt           0.1029
>
>  _refine_ls_wR_factor_ref         0.2803
>
>  _refine_ls_wR_factor_gt          0.1990
>
>  _refine_ls_goodness_of_fit_ref   1.004
>
>  _refine_ls_restrained_S_all      1.004
>
>  _refine_ls_shift/su_max          0.000
>
>  _refine_ls_shift/su_mean         0.000
>
>
>
>  loop_
>
>  _atom_site_label
>
>  _atom_site_type_symbol
>
>  _atom_site_fract_x
>
>  _atom_site_fract_y
>
>  _atom_site_fract_z
>
>  _atom_site_U_iso_or_equiv
>
>  _atom_site_adp_type
>
>  _atom_site_occupancy
>
>  _atom_site_symmetry_multiplicity
>
>  _atom_site_calc_flag
>
>  _atom_site_refinement_flags
>
>  _atom_site_disorder_assembly
>
>  _atom_site_disorder_group
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>  F1 F 0.0587(3) 0.1257(4) 0.09256(19) 0.0773(12) Uani 1 1 d . . .
>  F2 F -0.0926(3) 0.2839(3) 0.10355(19) 0.0796(13) Uani 1 1 d . . .
>  N1 N 0.0270(6) 0.3022(5) -0.0036(3) 0.0592(14) Uani 1 1 d . . .
>  N2 N 0.1431(5) 0.3421(4) 0.1373(3) 0.0582(15) Uani 1 1 d . . .
>  B1 B 0.0302(8) 0.2605(8) 0.0838(5) 0.062(2) Uani 1 1 d . . .
>  C1 C -0.0617(7) 0.2670(7) -0.0700(5) 0.076(2) Uani 1 1 d . . .
>  H1A H -0.1374 0.2152 -0.0703 0.092 Uiso 1 1 calc R . .
>  C2 C -0.0270(8) 0.3169(7) -0.1378(4) 0.076(2) Uani 1 1 d . . .
>  H2A H -0.0726 0.3045 -0.1904 0.092 Uiso 1 1 calc R . .
>  C3 C 0.0882(8) 0.3883(6) -0.1116(4) 0.0696(19) Uani 1 1 d . . .
>  H3A H 0.1350 0.4356 -0.1434 0.084 Uiso 1 1 calc R . .
>  C4 C 0.1228(7) 0.3776(6) -0.0288(4) 0.0583(17) Uani 1 1 d . . .
>  C5 C 0.2233(6) 0.4346(6) 0.0274(4) 0.0634(18) Uani 1 1 d . . .
>  H5A H 0.2867 0.4867 0.0099 0.076 Uiso 1 1 calc R . .
>  C6 C 0.2352(6) 0.4185(6) 0.1085(4) 0.0562(17) Uani 1 1 d . . .
>  C7 C 0.3230(7) 0.4738(6) 0.1728(5) 0.068(2) Uani 1 1 d . . .
>  H7A H 0.3941 0.5301 0.1700 0.082 Uiso 1 1 calc R . .
>  C8 C 0.2876(7) 0.4315(7) 0.2418(4) 0.075(2) Uani 1 1 d . . .
>  H8A H 0.3286 0.4536 0.2939 0.090 Uiso 1 1 calc R . .
>  C9 C 0.1766(7) 0.3482(6) 0.2168(4) 0.071(2) Uani 1 1 d . . .
>  H9A H 0.1324 0.3033 0.2510 0.085 Uiso 1 1 calc R . .
>
>
>
>  loop_
>
>  _atom_site_aniso_label
>
>  _atom_site_aniso_U_11
>
>  _atom_site_aniso_U_22
>
>  _atom_site_aniso_U_33
>
>  _atom_site_aniso_U_23
>
>  _atom_site_aniso_U_13
>
>  _atom_site_aniso_U_12
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>  F1 0.086(3) 0.061(3) 0.086(3) 0.008(2) 0.023(2) -0.007(2)
>  F2 0.055(2) 0.103(3) 0.089(3) -0.004(2) 0.0317(19) -0.010(2)
>  N1 0.057(4) 0.057(4) 0.065(4) 0.006(3) 0.017(3) 0.000(3)
>  N2 0.053(4) 0.058(4) 0.067(4) 0.008(3) 0.024(3) -0.007(3)
>  B1 0.053(6) 0.058(6) 0.080(6) 0.011(5) 0.026(5) 0.002(5)
>  C1 0.064(5) 0.088(6) 0.077(5) -0.003(4) 0.015(4) -0.014(4)
>  C2 0.083(6) 0.090(6) 0.059(5) 0.000(4) 0.023(4) 0.003(5)
>  C3 0.077(6) 0.066(5) 0.070(5) 0.012(4) 0.026(4) -0.002(4)
>  C4 0.049(5) 0.059(5) 0.068(5) 0.008(4) 0.015(4) 0.002(4)
>  C5 0.053(5) 0.062(5) 0.079(5) 0.018(4) 0.023(4) -0.003(4)
>  C6 0.059(5) 0.052(4) 0.058(5) 0.002(4) 0.013(4) -0.006(4)
>  C7 0.063(5) 0.066(5) 0.082(5) -0.004(4) 0.031(4) -0.007(4)
>  C8 0.055(5) 0.088(6) 0.076(5) -0.016(4) 0.000(4) 0.004(4)
>  C9 0.069(5) 0.100(6) 0.047(5) 0.019(4) 0.018(4) 0.003(4)
>
>
>
>  _geom_special_details
>  ;
>
>  All esds (except the esd in the dihedral angle between two l.s. planes)
>
>  are estimated using the full covariance matrix. The cell esds are taken
>
>  into account individually in the estimation of esds in distances, angles
>
>  and torsion angles; correlations between esds in cell parameters are only
>
>  used when they are defined by crystal symmetry. An approximate (isotropic)
>
>  treatment of cell esds is used for estimating esds involving l.s. planes.
>
>  ;
>
>
>
>  loop_
>
>  _geom_bond_atom_site_label_1
>
>  _geom_bond_atom_site_label_2
>
>  _geom_bond_distance
>
>  _geom_bond_site_symmetry_2
>
>  _geom_bond_publ_flag
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>  F1 B1 1.405(8) . ?
>  F2 B1 1.378(7) . ?
>  N1 C1 1.340(7) . ?
>  N1 C4 1.377(7) . ?
>  N1 B1 1.551(8) . ?
>  N2 C9 1.335(6) . ?
>  N2 C6 1.384(6) . ?
>  N2 B1 1.547(8) . ?
>  C1 C2 1.382(7) . ?
>  C1 H1A 0.9300 . ?
>  C2 C3 1.367(7) . ?
>  C2 H2A 0.9300 . ?
>  C3 C4 1.393(7) . ?
>  C3 H3A 0.9300 . ?
>  C4 C5 1.373(7) . ?
>  C5 C6 1.380(7) . ?
>  C5 H5A 0.9300 . ?
>  C6 C7 1.381(7) . ?
>  C7 C8 1.375(7) . ?
>  C7 H7A 0.9300 . ?
>  C8 C9 1.401(7) . ?
>  C8 H8A 0.9300 . ?
>  C9 H9A 0.9300 . ?
>
>
>
>  loop_
>
>  _geom_angle_atom_site_label_1
>
>  _geom_angle_atom_site_label_2
>
>  _geom_angle_atom_site_label_3
>
>  _geom_angle
>
>  _geom_angle_site_symmetry_1
>
>  _geom_angle_site_symmetry_3
>
>  _geom_angle_publ_flag
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>  C1 N1 C4 105.8(5) . . ?
>  C1 N1 B1 128.2(6) . . ?
>  C4 N1 B1 125.8(6) . . ?
>  C9 N2 C6 107.1(5) . . ?
>  C9 N2 B1 128.7(6) . . ?
>  C6 N2 B1 124.1(5) . . ?
>  F2 B1 F1 108.6(6) . . ?
>  F2 B1 N2 110.7(6) . . ?
>  F1 B1 N2 110.7(6) . . ?
>  F2 B1 N1 110.8(6) . . ?
>  F1 B1 N1 109.5(6) . . ?
>  N2 B1 N1 106.6(6) . . ?
>  N1 C1 C2 111.8(6) . . ?
>  N1 C1 H1A 124.1 . . ?
>  C2 C1 H1A 124.1 . . ?
>  C3 C2 C1 105.7(6) . . ?
>  C3 C2 H2A 127.1 . . ?
>  C1 C2 H2A 127.1 . . ?
>  C2 C3 C4 107.8(6) . . ?
>  C2 C3 H3A 126.1 . . ?
>  C4 C3 H3A 126.1 . . ?
>  C5 C4 N1 118.9(6) . . ?
>  C5 C4 C3 132.1(7) . . ?
>  N1 C4 C3 108.8(6) . . ?
>  C4 C5 C6 123.3(6) . . ?
>  C4 C5 H5A 118.3 . . ?
>  C6 C5 H5A 118.3 . . ?
>  C5 C6 N2 120.3(6) . . ?
>  C5 C6 C7 131.3(7) . . ?
>  N2 C6 C7 108.3(6) . . ?
>  C8 C7 C6 108.5(6) . . ?
>  C8 C7 H7A 125.8 . . ?
>  C6 C7 H7A 125.8 . . ?
>  C7 C8 C9 105.5(6) . . ?
>  C7 C8 H8A 127.3 . . ?
>  C9 C8 H8A 127.3 . . ?
>  N2 C9 C8 110.7(6) . . ?
>  N2 C9 H9A 124.7 . . ?
>  C8 C9 H9A 124.7 . . ?
>
>
>
>  loop_
>
>  _geom_torsion_atom_site_label_1
>
>  _geom_torsion_atom_site_label_2
>
>  _geom_torsion_atom_site_label_3
>
>  _geom_torsion_atom_site_label_4
>
>  _geom_torsion
>
>  _geom_torsion_site_symmetry_1
>
>  _geom_torsion_site_symmetry_2
>
>  _geom_torsion_site_symmetry_3
>
>  _geom_torsion_site_symmetry_4
>
>  _geom_torsion_publ_flag
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>  C9 N2 B1 F2 53.6(9) . . . . ?
>  C6 N2 B1 F2 -130.6(6) . . . . ?
>  C9 N2 B1 F1 -66.9(8) . . . . ?
>  C6 N2 B1 F1 108.9(6) . . . . ?
>  C9 N2 B1 N1 174.2(5) . . . . ?
>  C6 N2 B1 N1 -10.0(8) . . . . ?
>  C1 N1 B1 F2 -53.0(9) . . . . ?
>  C4 N1 B1 F2 131.8(6) . . . . ?
>  C1 N1 B1 F1 66.8(8) . . . . ?
>  C4 N1 B1 F1 -108.4(6) . . . . ?
>  C1 N1 B1 N2 -173.5(6) . . . . ?
>  C4 N1 B1 N2 11.3(8) . . . . ?
>  C4 N1 C1 C2 0.0(7) . . . . ?
>  B1 N1 C1 C2 -175.9(6) . . . . ?
>  N1 C1 C2 C3 -0.9(8) . . . . ?
>  C1 C2 C3 C4 1.4(7) . . . . ?
>  C1 N1 C4 C5 176.1(5) . . . . ?
>  B1 N1 C4 C5 -7.8(9) . . . . ?
>  C1 N1 C4 C3 0.9(7) . . . . ?
>  B1 N1 C4 C3 177.0(5) . . . . ?
>  C2 C3 C4 C5 -175.9(7) . . . . ?
>  C2 C3 C4 N1 -1.5(7) . . . . ?
>  N1 C4 C5 C6 1.1(9) . . . . ?
>  C3 C4 C5 C6 175.1(6) . . . . ?
>  C4 C5 C6 N2 -0.1(9) . . . . ?
>  C4 C5 C6 C7 -175.4(6) . . . . ?
>  C9 N2 C6 C5 -177.9(5) . . . . ?
>  B1 N2 C6 C5 5.6(9) . . . . ?
>  C9 N2 C6 C7 -1.6(6) . . . . ?
>  B1 N2 C6 C7 -178.2(6) . . . . ?
>  C5 C6 C7 C8 176.3(6) . . . . ?
>  N2 C6 C7 C8 0.6(7) . . . . ?
>  C6 C7 C8 C9 0.6(7) . . . . ?
>  C6 N2 C9 C8 2.0(7) . . . . ?
>  B1 N2 C9 C8 178.4(6) . . . . ?
>  C7 C8 C9 N2 -1.6(7) . . . . ?
>
>
>
>  _diffrn_measured_fraction_theta_max 0.987
>
>  _diffrn_reflns_theta_full        24.77
>
>  _diffrn_measured_fraction_theta_full 0.987
>
>  _refine_diff_density_max         0.181
>
>  _refine_diff_density_min         -0.178
>
>  _refine_diff_density_rms         0.049
>
>
>
>
>
>
>  ########################################################################
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