Back to File Formats
CIF is the preferred input file format as it is a globally accepted standard format and most of the popular crystallographic structure solution packages now provide a CIF output option.
Not all of the CIF fields have to be provided, but in general it is best to provide as much data as is available. Do not include non-bonded or intermolecular distances in the CIF, as these cannot be stored in the CSD and will result in much 3D editing in PreQuest.
A concordance list of CIF fields that can be read by PreQuest is given below. As the program converts CIF data to the BCCAB format for ease of editing within PreQuest, the list is presented as BCCAB headings with the CIF data fields that pertain to them listed below.
If not then it will use _journal_page_first otherwise created from position of CIF file in total list.
If _journal_coden_Cambridge is not present then the program attempts to translates to the correct coden from _journal_coden_ASTM if present
If a journal is one that starts from 1 with each issue then _journal_issue is also used.
If available the data in _diffrn_ambient_temperature is used, if not then the data in _cell_measurement_temperature is used with a warning. In both cases temperatures in the range 293K +/-10K are not reported. If both are reported and are different by more than 10K a warning is reported.
Pressure used _diffrn_ambient_pressure
If a pressure is reported in the CIF then it is always translated into the BCCAB.
Radiation Type _diffrn_radiation_type
If radiation type is given as Neutron this is reported in #QUAL.
Crystal colour is obtained from _exptl_crystal_colour
Initially _chemical_compound_source was used but this has been removed due to vagaries of the information that was stored there.
_cell_length_a _cell_length_b _cell_length_c _cell_angle_alpha _cell_angle_beta _cell_angle_gamma _symmetry_cell_settingZ value from _cell_formula_units_Z
Space group from _symmetry_space_group_name_H-M
Cell volume from _cell_volume
Diffraction density from _exptl_crystal_density_diffrn
Chemical formula weight from _chemical_formula_weight
_refine_ls_R_factor_all _refine_ls_R_factor_obs _refine_ls_wR_factor_all _refine_ls_wR_factor_obs
If both are present then _chemical_name_systematic goes into #COMPND and _chemical_name_common goes into #SYNONM.
If only one is present this is put in #COMPND. If the only one is _chemical_name_common then a warning is put into #RMARKS.
If neither is present then the title _publ_section_title if present, is used.
If this is not present then _publ_section_abstract is used.
_atom_site_label _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z
_geom_bond_atom_site_label_1 _geom_bond_atom_site_label_2 _geom_bond_distance _geom_bond_site_symmetry_1 _geom_bond_site_symmetry_2
and if not present from _chemical_formula_sum
If this is not present then from _chemical_formula_iucr
and if this is not present then from _chemical_formula_structural
In addition the following text blocks are searched:
_publ_section_title _publ_section_abstract _publ_section_comment _publ_section_experimental _publ_section_discussion _publ_section_exptl_prep _publ_section_exptl_refinementfor the following words or parts thereof:
disorder-,occupanc-, mp,M.p,Mp., isostructural,isomorphous, Deuter-, guest,host,inclusion,clathrate, hydroscopic,moisture,decompose, absolute,optical,Friedel, anomalous,dispersion,Bijvoet,Hamilton,eta,Roger, R-factor,ratio,Flack,activit-,inhibitor, agent,drug,medic-,-agonist,biological,bacteri-, -microbial,-viral,pharmac-,therapeut-The complete contents of the following are dumped:
_refine_ls_abs_structure_details _refine_ls_abs_structure_Flackand any non-unitary values of _atom_site_occupancy are identified up to a preset limit.
