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4.1 CIF

The Crystallographic Information File is documented fully by Hall, Allen & Brown (Acta Cryst., 1991, A47, 655-685).

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.

REFCODE

From _database_code_CSD if present.

If not then it will use _journal_page_first otherwise created from position of CIF file in total list.

#JRNL

From _journal_coden_Cambridge, _journal_volume, _journal_page_first, _journal_year

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.

#AUTH

The only data name used is _publ_author_name

#DISORD

Nothing done at the current time.

#QUAL

Temperature used _diffrn_ambient_temperature and _cell_measurement_temperature

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.

#PROPS

Melting point is obtained from _chemical_melting_point

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

Main cell data is obtained from:

  _cell_length_a
  _cell_length_b
  _cell_length_c
  _cell_angle_alpha
  _cell_angle_beta
  _cell_angle_gamma
  _symmetry_cell_setting
Z value from _cell_formula_units_Z

Space group from _symmetry_space_group_name_H-M

Cell volume from _cell_volume

#DENSITY

Measure density no longer archived.

Diffraction density from _exptl_crystal_density_diffrn

Chemical formula weight from _chemical_formula_weight

#SYSCAT

The crystal system is determined during #CELL processing.

#RFACT

The lowest (non-zero) value of the following is used for #RFACT:

  _refine_ls_R_factor_all
  _refine_ls_R_factor_obs
  _refine_ls_wR_factor_all
  _refine_ls_wR_factor_obs

#UNIS

Currently only the "template" is included in the BCCAB file.

#CLASS

Currently only the stub "#CLASS" is output.

#COMPND & #SYNONM

The following datanames are examined _chemical_name_systematic, _chemical_name_common

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

Atom data is obtained from:

  _atom_site_label
  _atom_site_fract_x
  _atom_site_fract_y
  _atom_site_fract_z

#BOND

Bond data is obtained from:

  _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

#FORMUL

Formula data is obtained from _chemical_formula_moiety

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

#CONN, #CREF, #CRYCON, #DIAGRAM, #RADIUS and #SYMM

Nothing done at the current time.

#RMARKS

Various informational and warning messages are stored in #RMARKS.

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_refinement
for 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_Flack
and any non-unitary values of _atom_site_occupancy are identified up to a preset limit.

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PreQuest: 4.2 SHELX .