I have been trying to build a supercell of the following (below) two molecular crystals from their .cif file. How do I sort a supercell here according to each molecule? What I want is an output file with all of the atoms, in a specified order, for molecule 1, followed by all of the atoms in the same specified order, for molecule 2, and so on (ideally, in the following order: H, H, H, C bonded to H, central C, N). How do I do this?
A solution for a single molecule was generously suggested to me on another forum, but when I try to adapt it to a supercell, I am still able to print only a single molecule.
_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