5
$\begingroup$

I am trying to use ASE (Atomic Simulation Environment) to build a supercell of some molecular crystals and then output the result to a file with the atoms given in a specified order for each molecule, followed by the second molecule, and so on.

When I import the .cif files, I get the following warnings (below). What should I do about them?

UserWarning: crystal system 'monoclinic' is not interpreted for space group Spacegroup(14, setting=1). This may result in wrong setting!

UserWarning: crystal system 'orthorhombic' is not interpreted for space group Spacegroup(36, setting=1). This may result in wrong setting!

The cif file for the two crystal structures is:

_audit_creation_method     SHELXL
_journal_date_recd_electronic     2002-06-07
_journal_date_accepted     2002-09-25
_journal_name_full     'Acta Crystallographica, Section B'
_journal_year     2002
_journal_volume     58
_journal_issue      6
_journal_page_first     1005
_journal_page_last     1010
_journal_paper_category     FA
_chemical_name_systematic     'acetonitrile'
_chemical_name_common     ?
_chemical_formula_moiety     'C2 H3 N'
_chemical_formula_sum     'C2 H3 N'
_chemical_formula_structural     'C H3 C N'
_chemical_formula_analytical     ?
_chemical_formula_weight     41.05
_chemical_melting_point     ?
_symmetry_cell_setting     'orthorhombic'
_symmetry_space_group_name_H-M     'C m c 21'
_symmetry_space_group_name_Hall     'C 2c -2'
loop_
    _symmetry_equiv_pos_as_xyz
    'x, y, z'
    '-x, -y, 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'
    '-x+1/2, y+1/2, z'
    'x+1/2, -y+1/2, z+1/2'
_cell_length_a     6.1870(10)
_cell_length_b     5.282(3)
_cell_length_c     7.887(4)
_cell_angle_alpha     90.00
_cell_angle_beta     90.00
_cell_angle_gamma     90.00
_cell_volume     257.7(2)
_cell_formula_units_Z     4
_cell_measurement_reflns_used     25
_cell_measurement_theta_min     5.68
_cell_measurement_theta_max     20.11
_cell_measurement_temperature     206(2)
_exptl_crystal_description     'cylinder'
_exptl_crystal_colour     'colourless'
_exptl_crystal_size_max     1.2
_exptl_crystal_size_mid     0.5
_exptl_crystal_size_min     0.3
_exptl_crystal_size_rad     0.15
_exptl_crystal_density_diffrn     1.058
_exptl_crystal_density_meas     ?
_exptl_crystal_density_method     ?
_exptl_crystal_F_000     88
_exptl_absorpt_coefficient_mu     0.069
_exptl_absorpt_correction_type     'none'
_exptl_absorpt_correction_T_min     ?
_exptl_absorpt_correction_T_max     ?
_exptl_special_details
;
 ?
;
_diffrn_ambient_temperature     206(2)
_diffrn_radiation_type     MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_radiation_source     'fine-focus sealed tube'
_diffrn_radiation_monochromator     graphite
_diffrn_measurement_device     'Nonius CAD4 diffractometer'
_diffrn_measurement_method     '\w--2\q'
_diffrn_reflns_number     136
_diffrn_reflns_av_R_equivalents     0.0000
_diffrn_reflns_av_sigmaI/netI     0.0473
_diffrn_reflns_theta_min     5.06
_diffrn_reflns_theta_max     24.91
_diffrn_reflns_theta_full     24.91
_diffrn_measured_fraction_theta_max     0.99
_diffrn_measured_fraction_theta_full     0.99
_diffrn_reflns_limit_h_min     0
_diffrn_reflns_limit_h_max     7
_diffrn_reflns_limit_k_min     0
_diffrn_reflns_limit_k_max     6
_diffrn_reflns_limit_l_min     -9
_diffrn_reflns_limit_l_max     0
_diffrn_standards_number     'none'
_diffrn_standards_interval_count     'none'
_diffrn_standards_interval_time     'none'
_diffrn_standards_decay_%     'none'
_refine_special_details
;
 Refinement of F^2^ against ALL reflections.  Weighted R-factors wR and
 goodnesses 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.
;
_reflns_number_total     136
_reflns_number_gt     99
_reflns_threshold_expression     'I>2\s(I)'
_refine_ls_structure_factor_coef     Fsqd
_refine_ls_matrix_type     full
_refine_ls_R_factor_all     0.0891
_refine_ls_R_factor_gt     0.0580
_refine_ls_wR_factor_all     0.1899
_refine_ls_wR_factor_ref     0.1492
_refine_ls_goodness_of_fit_all     1.200
_refine_ls_goodness_of_fit_ref     1.155
_refine_ls_restrained_S_all     1.200
_refine_ls_restrained_S_obs     1.155
_refine_ls_number_reflns     136
_refine_ls_number_parameters     26
_refine_ls_number_restraints     0
_refine_ls_hydrogen_treatment     'refall'
_refine_ls_weighting_scheme     calc
_refine_ls_weighting_details
              'w=1/[\s^2^(Fo^2^)+(0.0888P)^2^+0.1685P] where P=(Fo^2^+2Fc^2^)/3'
_atom_sites_solution_hydrogens     difmap
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary     difmap
_refine_ls_shift/su_max     0.037
_refine_ls_shift/su_mean     0.001
_refine_diff_density_max     0.176
_refine_diff_density_min     -0.172
_refine_ls_extinction_method     SHELXL
_refine_ls_extinction_coef     0.01(7)
_refine_ls_extinction_expression
                                  'Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^'
_refine_ls_abs_structure_details
                                    'Flack H D (1983), Acta Cryst. A39, 876-881'
_refine_ls_abs_structure_Flack     -10(10)
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'
    'N' 'N' 0.0061 0.0033
                         'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
_computing_data_collection     'CAD4-EXPRESS (Enraf-Nonius, 1993)'
_computing_cell_refinement     'CAD4-EXPRESS (Enraf-Nonius, 1993)'
_computing_data_reduction     'CADAK (Savariault,1991)'
_computing_structure_solution     'SHELXS-96 (Sheldrick, 1990)'
_computing_structure_refinement     'SHELXL-96 (Sheldrick, 1996)'
_computing_molecular_graphics     'ORTEP III (Burnett & Johnson, 1996)'
_computing_publication_material     'SHELXL-96 (Sheldrick, 1996)'
loop_
    _atom_site_label
    _atom_site_fract_x
    _atom_site_fract_y
    _atom_site_fract_z
    _atom_site_U_iso_or_equiv
    _atom_site_thermal_displace_type
    _atom_site_calc_flag
    _atom_site_refinement_flags
    _atom_site_occupancy
    _atom_site_disorder_group
    _atom_site_type_symbol
    N 0.0000 0.4380(14) -0.0974(18) 0.070(3) Uani d S 1 . N
    C1 0.0000 0.0776(15) 0.1243(18) 0.053(2) Uani d S 1 . C
    C2 0.0000 0.2762(16) 0.0000 0.053(2) Uani d S 1 . C
    H1 0.0000 -0.104(15) 0.080(12) 0.07(3) Uiso d S 1 . H
    H2 0.149(11) 0.087(9) 0.201(8) 0.083(19) Uiso d . 1 . H
loop_
    _atom_site_aniso_label
    _atom_site_aniso_U_11
    _atom_site_aniso_U_22
    _atom_site_aniso_U_33
    _atom_site_aniso_U_12
    _atom_site_aniso_U_13
    _atom_site_aniso_U_23
    N 0.070(5) 0.069(6) 0.070(6) 0.000 0.000 0.014(4)
    C1 0.058(5) 0.050(4) 0.052(5) 0.000 0.000 0.008(5)
    C2 0.035(3) 0.067(4) 0.058(4) 0.000 0.000 -0.011(5)
_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_site_symmetry_2
    _geom_bond_distance
    _geom_bond_publ_flag
    N C2 . 1.149(12) yes
    C1 C2 . 1.436(12) yes
    C1 H1 . 1.02(8) yes
    C1 H2 . 1.11(7) yes
loop_
    _geom_angle_atom_site_label_1
    _geom_angle_atom_site_label_2
    _geom_angle_atom_site_label_3
    _geom_angle_site_symmetry_1
    _geom_angle_site_symmetry_3
    _geom_angle
    _geom_angle_publ_flag
    C2 C1 H1 . . 117(6) yes
    C2 C1 H2 . . 110(3) yes
    H1 C1 H2 . . 103(4) yes
    N C2 C1 . . 178.9(12) yes
data_II
_audit_creation_method     SHELXL
_chemical_name_systematic     'acetonitrile'
_chemical_name_common     ?
_chemical_formula_moiety     'C2 H3 N'
_chemical_formula_sum     'C2 H3 N'
_chemical_formula_structural     'C H3 C N'
_chemical_formula_analytical     ?
_chemical_formula_weight     41.05
_chemical_melting_point     ?
_symmetry_cell_setting     'monoclinic'
_symmetry_space_group_name_H-M     'P 21/c'
_symmetry_space_group_name_Hall     '-P 2ybc'
loop_
    _symmetry_equiv_pos_as_xyz
    'x, y, z'
    '-x, y+1/2, -z+1/2'
    '-x, -y, -z'
    'x, -y-1/2, z-1/2'
_cell_length_a     4.102(3)
_cell_length_b     8.244(7)
_cell_length_c     7.970(7)
_cell_angle_alpha     90.00
_cell_angle_beta     100.10(10)
_cell_angle_gamma     90.00
_cell_volume     265.3(4)
_cell_formula_units_Z     4
_cell_measurement_reflns_used     25
_cell_measurement_theta_min     5.20
_cell_measurement_theta_max     21.48
_cell_measurement_temperature     201(2)
_exptl_crystal_description     'cylinder'
_exptl_crystal_colour     'colourless'
_exptl_crystal_size_max     1.2
_exptl_crystal_size_mid     0.5
_exptl_crystal_size_min     0.3
_exptl_crystal_size_rad     0.15
_exptl_crystal_density_diffrn     1.028
_exptl_crystal_density_meas     ?
_exptl_crystal_density_method     ?
_exptl_crystal_F_000     88
_exptl_absorpt_coefficient_mu     0.067
_exptl_absorpt_correction_type     'none'
_exptl_absorpt_correction_T_min     ?
_exptl_absorpt_correction_T_max     ?
_exptl_special_details
;
 ?
;
_diffrn_ambient_temperature     201(2)
_diffrn_radiation_type     MoK\a
_diffrn_radiation_wavelength     0.71073
_diffrn_radiation_source     'fine-focus sealed tube'
_diffrn_radiation_monochromator     'graphite'
_diffrn_measurement_device     'Nonius CAD4 diffractometer'
_diffrn_measurement_method     '\w--2\q'
_diffrn_reflns_number     376
_diffrn_reflns_av_R_equivalents     0.0571
_diffrn_reflns_av_sigmaI/netI     0.0591
_diffrn_reflns_theta_min     3.58
_diffrn_reflns_theta_max     21.89
_diffrn_reflns_theta_full     21.89
_diffrn_measured_fraction_theta_max     0.99
_diffrn_measured_fraction_theta_full     0.99
_diffrn_reflns_limit_h_min     0
_diffrn_reflns_limit_h_max     4
_diffrn_reflns_limit_k_min     0
_diffrn_reflns_limit_k_max     8
_diffrn_reflns_limit_l_min     -8
_diffrn_reflns_limit_l_max     8
_diffrn_standards_number     'none'
_diffrn_standards_interval_count     'none'
_diffrn_standards_interval_time     'none'
_diffrn_standards_decay_%     'none'
_refine_special_details
;
 Refinement of F^2^ against ALL reflections.  Weighted R-factors wR and
 goodnesses 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.
;
_reflns_number_total     324
_reflns_number_gt     202
_reflns_threshold_expression     'I>2\s(I)'
_refine_ls_structure_factor_coef     Fsqd
_refine_ls_matrix_type     full
_refine_ls_R_factor_all     0.1051
_refine_ls_R_factor_gt     0.0472
_refine_ls_wR_factor_all     0.1504
_refine_ls_wR_factor_ref     0.1106
_refine_ls_goodness_of_fit_all     1.137
_refine_ls_goodness_of_fit_ref     1.107
_refine_ls_restrained_S_all     1.137
_refine_ls_restrained_S_obs     1.107
_refine_ls_number_reflns     324
_refine_ls_number_parameters     41
_refine_ls_number_restraints     0
_refine_ls_hydrogen_treatment     'refall'
_refine_ls_weighting_scheme     calc
_refine_ls_weighting_details
              'w=1/[\s^2^(Fo^2^)+(0.0360P)^2^+0.1879P] where P=(Fo^2^+2Fc^2^)/3'
_atom_sites_solution_hydrogens     difmap
_atom_sites_solution_primary     direct
_atom_sites_solution_secondary     difmap
_refine_ls_shift/su_max     0.000
_refine_ls_shift/su_mean     0.000
_refine_diff_density_max     0.169
_refine_diff_density_min     -0.168
_refine_ls_extinction_method     SHELXL
_refine_ls_extinction_coef     0.07(4)
_refine_ls_extinction_expression
                                  'Fc^*^=kFc[1+0.001xFc^2^\l^3^/sin(2\q)]^-1/4^'
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'
    'N' 'N' 0.0061 0.0033
                         'International Tables Vol C Tables 4.2.6.8 and 6.1.1.4'
_computing_data_collection     'CAD4-EXPRESS (Enraf-Nonius, 1993)'
_computing_cell_refinement     'CAD4-EXPRESS (Enraf-Nonius, 1993)'
_computing_data_reduction     'CADAK (Savariault,1991)'
_computing_structure_solution     'SHELXS-96 (Sheldrick, 1990)'
_computing_structure_refinement     'SHELXL-96 (Sheldrick, 1996)'
_computing_molecular_graphics     'ORTEP III (Burnett & Johnson, 1996)'
_computing_publication_material     'SHELXL-96 (Sheldrick, 1996)'
loop_
    _atom_site_label
    _atom_site_fract_x
    _atom_site_fract_y
    _atom_site_fract_z
    _atom_site_U_iso_or_equiv
    _atom_site_thermal_displace_type
    _atom_site_calc_flag
    _atom_site_refinement_flags
    _atom_site_occupancy
    _atom_site_disorder_group
    _atom_site_type_symbol
    N 0.4547(9) 0.2657(5) 0.4613(4) 0.0710(15) Uani d . 1 . N
    C1 0.0949(12) 0.4579(6) 0.2478(6) 0.0586(14) Uani d . 1 . C
    C2 0.2946(9) 0.3498(5) 0.3672(5) 0.0507(13) Uani d . 1 . C
    H1 -0.108(11) 0.402(5) 0.166(5) 0.089(14) Uiso d . 1 . H
    H2 0.233(11) 0.518(6) 0.186(6) 0.113(18) Uiso d . 1 . H
    H3 -0.050(11) 0.538(6) 0.301(5) 0.103(16) Uiso d . 1 . H
loop_
    _atom_site_aniso_label
    _atom_site_aniso_U_11
    _atom_site_aniso_U_22
    _atom_site_aniso_U_33
    _atom_site_aniso_U_12
    _atom_site_aniso_U_13
    _atom_site_aniso_U_23
    N 0.076(3) 0.070(3) 0.064(2) 0.005(2) 0.0028(18) 0.008(2)
    C1 0.058(3) 0.060(3) 0.055(3) 0.005(2) 0.001(2) 0.008(2)
    C2 0.056(2) 0.050(3) 0.047(2) -0.007(2) 0.0101(19) -0.009(2)
_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_site_symmetry_2
    _geom_bond_distance
    _geom_bond_publ_flag
    N C2 . 1.141(5) yes
    C1 C2 . 1.448(6) yes
    C1 H1 . 1.07(5) yes
    C1 H2 . 0.96(5) yes
    C1 H3 . 1.03(5) yes
loop_
    _geom_angle_atom_site_label_1
    _geom_angle_atom_site_label_2
    _geom_angle_atom_site_label_3
    _geom_angle_site_symmetry_1
    _geom_angle_site_symmetry_3
    _geom_angle
    _geom_angle_publ_flag
    C2 C1 H1 . . 115(2) yes
    C2 C1 H2 . . 110(3) yes
    H1 C1 H2 . . 112(3) yes
    C2 C1 H3 . . 115(2) yes
    H1 C1 H3 . . 95(3) yes
    H2 C1 H3 . . 108(4) yes
    N C2 C1 . . 179.3(4) yes
$\endgroup$
6
  • 1
    $\begingroup$ +1 But I've narrowed your question down to just 1, since we have a policy to only allow 1 question per post. You're always welcome to ask the second question in a new post though! $\endgroup$ Mar 7 at 21:02
  • 1
    $\begingroup$ @NikeDattani Thanks for letting me know, and for making it a better question. $\endgroup$
    – user1
    Mar 7 at 21:13
  • 2
    $\begingroup$ Can you post a CIF file that causes a problem? $\endgroup$ Mar 8 at 14:20
  • 2
    $\begingroup$ @user1 Can you please either copy and paste the CIF into a code block if it's fewer than a few thousand lines long, or upload it here: github.com/HPQC-LABS/Modeling_Matters in a folder called 4457 since this question is post number 4457? $\endgroup$ Mar 8 at 18:45
  • 2
    $\begingroup$ @user1 I have pinged the ASE element chat, maybe someone can get you an answer. I am not sure anyone on this SE currently works on the CIF parser actively, but maybe its a more obvious error than I realize $\endgroup$ Mar 8 at 21:01
7
$\begingroup$

As far as I understand, this warning can be safely ignored. While parsing a cif structure, the get_spacegroup() function in the cif parser of ASE, checks whether the space group evaluated by ASE is consistent with the cell symmetry mentioned in the cif file. The relevant part of the function is shown below:

if setting_name:
            no = Spacegroup(spacegroup).no
            if no in rhombohedral_spacegroups:
                if setting_name == 'hexagonal':
                    setting = 1
                elif setting_name in ('trigonal', 'rhombohedral'):
                    setting = 2
                else:
                    warnings.warn(
                        'unexpected crystal system %r for space group %r' % (
                            setting_name, spacegroup))
            # FIXME - check for more crystal systems...
            else:
                warnings.warn(
                    'crystal system %r is not interpreted for space group %r. '
                    'This may result in wrong setting!' % (
                        setting_name, spacegroup))

Here, setting_name denotes the cell symmetry setting mentioned in the cif file and no is the space group of the structure as evaluated by ASE. As can be seen this check has been currently implemented only for rhombohedral crystal systems and for any other crystal systems it shows the warning in the question (notice the comment: # FIXME - check for more crystal systems...). When the checks are implemented for other crystal symmetries the warnings will also go away.

For the warnings in the question, it can be manually verified that the spacegroup numbers are consistent with the cell symmetry mentioned in the cif file. For eg, from here.

$\endgroup$
0

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