.. _manual_cif: 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| ` 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``.