CIF (Crystallographic Information Format) files#

Reading CIF files#

Fox can import CIF files. For more information about CIF (Crystallographic Information File), see the International Union of Crystallography website. Note that Fox only supports part of the CIF standard: it should be able to parse correctly CIF files, but will interpret only part of the CIF data - those useful to extract a crystal structure or a powder pattern. Therefore Fox should not be used to validate CIF files.

CIF files can be imported from the command line as any Fox .xml, e.g. Fox pbso4.cif will parse the pbso4.cif file for crystal structure(s) or powder patterns, and will create the corresponding objects. This also implies that in file browsers, it is possible to right-click on a CIF file and choose open with Fox to open the file. On some systems, drag & drop of cif files on the Fox application icon should also work. Several files can also be suuplied at once…

Additionally, when opening a CIF file, if in the :ref:`Preferences| <manual_preferences>` you have specified to automatically open the 3D crystal view and the powder pattern graph, you will immediately see what your structure/data looks like !

Importing crystal structures from CIF#

To extract a crystal structure only parts of the core cif dictionnary are recognized.

CIF tags currently recognized include (“tag1 > tag2” means tag1 is preferred to tag2 when extracting the info, only one is used):

  • crystal name: _chemical_name_systematic > _chemical_name_mineral > _chemical_name_structure_type > _chemical_name_common

  • crystal formula: _chemical_formula_analytical > _chemical_formula_structural > _chemical_formula_iupac > _chemical_formula_moiety

  • unit cell: _cell_length_{a,b,c} ; _cell_angle_{alpha,beta,gamma}

  • spacegroup number: _space_group_IT_number > _symmetry_Int_Tables_number

  • spacegroup Hall symbol: _space_group_name_Hall > _symmetry_space_group_name_Hall

  • spacegroup Hermann-Mauguin symbol: _space_group_name_H-M_alt > _symmetry_space_group_name_H-M

  • atom coordinates: _atom_site_fract_{x} ; _atom_site_Cartn_{x,y,z}

  • atom occupancy: _atom_site_occupancy

  • atom label & symbol: _atom_site_type_symbol ; _atom_site_label

Importing powder patterns from CIF#

To import powder pattern data, the following tags are used from the powder CIF dictionnary (pdCIF):

  • observed intensity: _pd_meas_counts_total > _pd_meas_intensity_total > _pd_proc_intensity_total > _pd_proc_intensity_net

  • uncertainty on intensity: deducted from _pd_proc_ls_weight or equal to the square root of the observed intensity

  • coordinates: _pd_proc_2theta_corrected > _pd_meas_angle_2theta > _pd_meas_time_of_flight > _pd_proc_2theta_range_{min,max,inc} > _pd_meas_2theta_range_{min,max,inc}

  • intensity normalizer (optional): _pd_meas_intensity_monitor > _pd_meas_step_count_time

  • wavelength:_diffrn_radiation_wavelength > _pd_proc_wavelength.

Note: unfortunately, the wavelength is generally not present in powder CIF (!), but is listed in the crystal structure CIF. However, whenever Fox finds a new wavelength in a CIF file, it stores it as a static variable, to be used as the default wavelength. So if you read your CIF files by giving as input both the crystal structure file (with the wavelength) and the powder pattern CIF, the correct wavelength will be assigned to the powder pattern object. This assumes that the wavelength is read before the powder pattern, i.e. listed before on the command line: `` Fox structure.cif powderdata.cif``

Importing single crystal data from CIF#

To import single crystal data, the following tags are recognized:

  • observed intensity: _refln_F_squared_meas

  • sigma (not required): _refln_F_squared_sigma

  • h, k, l: _refln_index_h, _refln_index_k, _refln_index_l

  • wavelength:_diffrn_radiation_wavelength > _pd_proc_wavelength.