Authors: Doug du Boulay & Syd Hall
Contact: Syd Hall, Crystallography Centre, University of Western Australia, Nedlands 6907, Australia
PREPUB performs a subset of the IUCr data validation series of CIF tests on all data blocks of a supplied CIF containing structural data.
A series of checks are made on a CIF containing one or more data blocks. The following tests are applied:
Test that the data organisation of the CIF conforms to the STAR syntax. Mismatched tags and values are identified, as well as unclosed text blocks, and whether items are missing from a looped list.
Check that the data items in the CIF are defined in the standard CoreCIF dictionary.
SYMMG01 DVtest: Check the _symmetry_space_group_number value matches that expected for the _symmetry_space_group_name_H-M entry.
SYMMG02 DVtest: Check that the _symmetry_equiv_pos_as_xyz values are consistent with the _symmetry_space_group_name_H-M entry.
CELLZ01 DVtest: Check that the combination of the _cell_formula_units_Z number and the _chemical_formula_sum entry matches the atomic content derived from the atomic site information in the _atom_site list.
CHEMW03 DVtest: Check that the _chemical_formula_weight value matches that calculated from the atomic site information in the _atom_site list.
REFLT03 DVtest: Check that the calculated number of reflections in the diffraction sphere out to the _diffrn_reflns_theta_max value is consistent with the number reported in the CIF by _reflns_number_total. Checks are made on the _diffrn_reflns_limit_ max and min values, and the presence of Friedel pairs.
STRVAL02 DVtest: Check that the _refine_ls_abs_structure_Flack value is in a sensible range.
A typical input sequence is as follows, assuming a CIF filename is banana.cif
This results in an output, such as:
PREPUB banana 16-Mar99 Page 1 Xtal3.6 FEB97:UNXDEC ******************** *** Begin PREPUB *** ******************** INPUT FILE: banana.cif >>>>> Check input data names against dictionary. ciftbx warning: banana.cif data_global line: 38 Data name _iucr_compatibility_tag not in dictionary! ciftbx warning: banana.cif data_global line: 38 No category defined for _iucr_compatibility_tag ciftbx warning: banana.cif data_banana line: 342 Numb type violated _exptl_crystal_density_meas >>>>> End of CIF dictionary checking. =========================================================================== >>>>>>>>>>>>>>>>> Data block: global =========================================================================== >>>>>>>>>>>>>>>>> Data block: banana SYMMG_01: Check the space group number -------------------------------------- From the CIF: _symmetry_space_group_number ? From the CIF: _symmetry_space_group_name_H-M P n a 21 International Tables space group number for P n a 21 is 33 SYMMG_01: OK SYMMG_02: Check the space group is recognised --------------------------------------------- From the CIF: _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 The xyz symops generate the Hall space group symbol p_2c_-2n The xyz symops consistent with the H-M space group P_n_a_21 From the CIF: _symmetry_space_group_name_H-M p_n_a_21 SYMMG_02: OK CELLZ_01: Check formula with the supplied model ----------------------------------------------- From the CIF: _cell_formula_units_Z 4 From the CIF: _chemical_formula_sum Mo4 O11 TEST: Compare cell contents of formula and atom_site data atom Z*formula cif sites diff Mo 16.00 16.00 0.00 O 44.00 44.00 0.00 CELLZ_01: OK CHEMW_03: Check formula weight with the model --------------------------------------------- From the CIF: _cell_formula_units_Z 4 From the CIF: _chemical_formula_weight 559.76 TEST: Calculate formula weight from _atom_site_* atom mass num sum O 16.00 11.00 175.99 Mo 95.94 4.00 383.76 Calculated formula weight 559.75 CHEMW_03: OK REFLT_03: Check the reflection counts ------------------------------------- From the CIF: _diffrn_reflns_theta_max 29.99 From the CIF: _reflns_number_total 2267 From the CIF: _diffrn_reflns_limit_ max hkl 33. 9. 7. From the CIF: _diffrn_reflns_limit_ min hkl 0. 0. -7. TEST1: Expected hkl limits for theta max Calculated maximum hkl 33. 9. 7. Calculated minimum hkl -33. -9. -7. TEST2: Reflns within _diffrn_reflns_theta_max Count of symmetry unique reflns 1373 Completeness (_total/calc) 165.11% TEST3: Check Friedels for noncentro structure Estimate of Friedel pairs measured 894 Fraction of Friedel pairs measured 0.651 Are heavy atom types Z>Si present yes REFLT_03: OK STRVAL_02: Check absolute structure measures -------------------------------------------- From the CIF: _refine_ls_abs_structure_Flack 0.390 From the CIF: _refine_ls_abs_structure_Flack_su 0.070 ALERT: Flack test results are ambiguous. Time h m s CPU secs Total CPU secs Memory words 12:29:53 9.26126 9.40571 201001 |