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INTERNATIONAL TABLES for CRYSTALLOGRAPHY |
Volume G |
Definition and Exchange of Crystallographic Data |
In addition to the syntax description, a number of other documents were circulated to describe the evolving proposal. In this document, the list of standard data names was presented as a compact glossary, with indications of acceptable alternative physical units (this facility was later removed) and with summaries of permitted standard codes for some individual items.
CIF Document: #2 Version Oct22-89
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*** CIF Glossary of Data Names ***
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Syd Hall, Max-Planck-Institut fuer Kohlenforschung,
Mulheim/Ruhr, F.R.G.
Frank Allen, Cambridge Crystallographic Data Centre,
Cambridge University, Cambridge, U.K.
David Brown, McMaster University, Hamilton, Canada.
The IUCr Working Party on Crystallographic Information has proposed that
the IUCr establish facilities for receiving, archiving and transmitting
machine-readible crystallographic information suitable for --
1. publication in journals (e.g. Acta Crystallographica),
2. deposition of (secondary) data associated with 1., and
3. as a data source for existing and future data bases.
This data will be contained in a 'Crystallographic Information File' (CIF)
which uses a STAR file format (see CIF Document #1). The format of a STAR file
is sufficiently flexible to provide for present and future crystallographic
data requirements, and is virtually incorruptable. The specification of the
data, and its organisation, is contained within the STAR file itself. Software
for retrieving data from a STAR file is already available for local applications.
Because a STAR file is self-defining, a CIF will also be suitable for local
archiving of structure results. It will permit each laboratory, or program
package, to store any local data items in addition to those required for
the standard crystallographic publications or data bases.
In most cases a CIF will be generated by software. The major crystallographic
package developers have agreed to provide software that will generate CIF's
directly from their working files. The generated CIF's will probably contain
prompts for the information that should be added later for publication
purposes (e.g. manuscript text, etc.). This data can be added using a normal
text editor, as required.
Read CIF Document #1 for detais of the STAR File syntax. The CIF Document #3
contains check list of CIF Glossary items which indicates the requirements
of crystallographic publications and data bases, and the data generated by
different program systems. The CIF Document #4 is the CIF Dictionary which
defines all the data names in the Glossary. The CIF Document #5 is a copy of
the first test submission of a CIF to Acta Crystallographica C and provides
a typical example of a CIF manuscript and data set.
The glossary that follows contains the 'data names' of data commonly used in
crystallographic publications and data bases. This glossary will be expanded
according to future requirements, but the currently defined data names must
not be changed if they are to be accessible for standard publication and
archival purposes. Note that all data items may be included in a repeated
(i.e. loop_) list but only those which are flagged with an asterisk '*' are
normally expected to be used in this way. Units attribute codes are given
when applicable. The first named code is the default. Examples of how the
data item is specified are given for some names. The complete definition of
each data name is provided in the CIF Dictionary.
CIF Glossary of Data Names
--------------------------
Publication data items
----------------------
_publ_author_name * # syntax: "O'Neil, James K."
_publ_author_address *
_publ_title
_publ_abstract
_publ_introduction
_publ_experimental
_publ_discussion
_publ_related_literature
_publ_acknowledgements
_publ_references
_publ_tables
_publ_figure_captions
_publ_manuscript
_publ_contact_letter
_publ_contact_author_address
_publ_contact_author_phone
_publ_contact_author_fax
_publ_contact_author_email
_publ_requested_journal
_publ_requested_coeditor_name
Journal data items (for internal use by journals staff)
------------------
_journal_coeditor_code
_journal_coeditor_name
_journal_coeditor_address
_journal_coeditor_phone
_journal_coeditor_fax
_journal_coeditor_email
_journal_coeditor_notes
_journal_techeditor_code
_journal_techeditor_name
_journal_techeditor_address
_journal_techeditor_phone
_journal_techeditor_fax
_journal_techeditor_email
_journal_techeditor_notes
_journal_date_recd_electronic
_journal_date_recd_hard_copy
_journal_date_recd_copyright
_journal_date_to_coeditor
_journal_date_from_coeditor
_journal_date_accepted
_journal_date_printers_first
_journal_date_printers_final
_journal_date_proofs_out
_journal_date_proofs_in
_journal_suppl_publ_number
_journal_suppl_publ_pages
_journal_name_full
_journal_coden_ASTM
_journal_coden_Cambridge
_journal_year
_journal_volume
_journal_issue
_journal_page_first
_journal_page_last
Data base codes (for internal use by data bases)
---------------
_data_base_code_CAS
_data_base_code_CSD
_data_base_code_ICSD
_data_base_code_PDF
_data_base_code_MDF
_data_base_code_NBS
Chemical Information data items
-------------------------------
_chemical_name_systematic # normally 'text' data
_chemical_name_common # 'copper iron disulphide'
_chemical_name_mineral # 'chalcopyrite'
_chemical_name_structure_type # 'sphalerite'
_chemical_formula_sum # 'C24 H20 As Cl'
_chemical_formula_moiety # 'C24 H20 As +,Cl -'
_chemical_formula_structural # '(C6 H5)4 As +,Cl -'
_chemical_formula_analytical # 'Fe2.45 Ni1.60 S4'
_chemical_formula_residue_seq # normally a 'text' list
_chemical_formula_weight _Dalt
_chemical_compound_source # 'Norilsk, U.S.S.R.'
_chemical_melting_point _K _C
Computing Applications data items
---------------------------------
_computing_data_collection # 'CAD4 software'
_computing_cell_refinement
_computing data reduction
_computing_structure_solution
_computing_structure_refinement
_computing_molecular_graphics
_computing_diagram_preparation
Crystal Cell data items
-----------------------
_cell_a _A _nm _pm
_cell_b _A _nm _pm
_cell_c _A _nm
_cell_alpha _deg _rad
_cell_beta _deg _rad
_cell_gamma _deg _rad
_cell_volume _A _nm _pm
_cell_special_details
_cell_formula_units_Z
_cell_measurement_temperature _K _C
_cell_measurement_pressure _gPa _kPa
_cell_measurement_radiation # 'Xrays'
_cell_measurement_wavelength _A _nm _pm
_cell_measurement_reflns_used
_cell_measurement_theta_min _deg _rad
_cell_measurement_theta_max _deg _rad
Crystal Symmetry data items
---------------------------
_symmetry_crystal_axes # 'monoclinic'
_symmetry_name_Hermann-Mauguin # 'P 1 21/n 1'
_symmetry_name_Hall # '-P 2yn'
_symmetry_name_Int_Tables_number
_symmetry_equiv_pos_as_xyz *
Experimental data items
-----------------------
_exptl_special_details
_exptl_crystal_description
_exptl_crystal_colour
_exptl_crystal_size_max _mm _cm
_exptl_crystal_size_mid _mm _cm
_exptl_crystal_size min _mm _cm
_exptl_crystal_density diffrn _g.cm _Mg.m _kg.m
_exptl_crystal_density measured _g.cm _Mg.m _kg.m
_exptl_crystal_F(000)
_exptl_crystal_face_h *
_exptl_crystal_face_k *
_exptl_crystal_face_l *
_exptl_crystal_face_perp_dist * _mm _cm
_exptl_crystal_face_diffr_phi * _deg _rad
_exptl_crystal_face_diffr_chi * _deg _rad
_exptl_crystal_face_diffr_psi * _deg _rad
_exptl_crystal_face_diffr_kappa * _deg _rad
_exptl_absorpt_coefficient mu _mm _cm
_exptl_absorpt_correction_type # see Standard Codes
_exptl_absorpt_correction_T_min
_exptl_absorpt_correction_T_max
Diffraction data items
----------------------
_diffrn_special_details
_diffrn_temperalture _K _C
_diffrn_pressure _gPa _kPa
_diffrn_radiation_wavelength _A _nm _pm
_diffrn_radiation_type # 'neutron'
_diffrn_radiation_source # 'synchrotron'
_diffrn_radiation_monochromator # 'graphite'
_diffrn_radiation_detector # 'scintillation'
_diffrn_camera_geometry # 'precession'
_diffrn_camera_model # 'Supper'
_diffrn_diffractometer_geometry # '4-circle'
_diffrn_diffractometer_model # 'CAD4'
_diffrn_measurement_process # 'bpb 2th_th bisecting'
_diffrn_orient_matrix_11
_diffrn_orient_matrix_21
_diffrn_orient_matrix_31
_diffrn_orient_matrix_12
_diffrn_orient_matrix_22
_diffrn_orient_matrix_32
_diffrn_orient_matrix_13
_diffrn_orient_matrix_23
_diffrn_orient_matrix_33
_diffrn_orient_refln_h *
_diffrn_orient_refln_k *
_diffrn_orient_refln_l *
_diffrn_orient_refln_phi * _deg _rad
_diffrn_orient_refln_chi * _deg _rad
_diffrn_orient_refln_psi * _deg _rad
_diffrn_orient_refln_kappa * _deg _rad
_diffrn_standards_h *
_diffrn_standards_k *
_diffrn_standards_l *
_diffrn_standards_number
_diffrn_standards_interval _refn _hour _min _sec
_diffrn_standards_decay_%
_diffrn_standards_scale_sigma
_diffrn_scale_group_code *
_diffrn_scale_I_net *
_diffrn_attenuator_code *
_diffrn_attenuator_scale *
_diffrn_refln_h *
_diffrn_refln_k *
_diffrn_refln_l *
_diffrn_refln_counts_total *
_diffrn_refln_counts_net *
_diffrn_refln_counts_bg_1 *
_diffrn refln_counts_bg 2 *
_diffrn_refln_counts_peak *
_diffrn_refln_scale_group_code * # see _diffrn_scale_group_code
_diffrn_refln_attenuator_code * # see _diffrn_attenuator_code
_diffrn_refln_intensity *
_diffrn_refln_intensity_sigma *
_diffrn_refln_sint/lambda * _A _nm _pm
_diffrn_refln_wave_length * _A _nm _pm
_diffrn_refln_theta * _deg _rad
_diffrn_refln_omega * _deg _rad
_diffrn_refln_phi * _deg _rad
_diffrn_refln_chi * _deg _rad
_diffrn_refln_psi * _deg _rad
_diffrn_refln_kappa * _deg _rad
_diffrn_reflns_reduction_process # usually text decription
_diffrn_reflns_theta_min _deg _rad
_diffrn_reflns_theta_max _deg _rad
_diffrn_reflns_h_min
_diffrn_reflns_h_max
_diffrn_reflns_k_min
_diffrn_reflns_k_max
_diffrn_reflns_l_min
_diffrn_reflns_l_max
_diffrn_reflns_number
_diffrn_reflns_merge_R_factor # e.g. 0.03 not 3.0 (%)
_diffrn_reflns_transf_matrix_11 # This is the matrix for
_diffrn_reflns_transf_matrix_21 # transforming the measured
_diffrn_reflns_transf_matrix_31 # diffraction hkl indices into
_diffrn_reflns_transf_matrix_12 # the hkl indices of the cell
_diffrn_reflns_transf_matrix_22 # given in list_cell.
_diffrn_reflns_transf_matrix_32 #
_diffrn_reflns_transf_matrix_13 # |11 12 13|
_diffrn_reflns_transf_matrix_23 # (meas h,k,1)|21 22 23|=(h,k,l)
_diffrn_reflns_transf_matrix_33 # |31 32 33|
Atom Type data types
--------------------
_atom_type_symbol # Ru
_atom_type_description # Ruthenium
_atom_type_number_in_cell # 8.0 (RU's in the cell)
_atom_type_radius_bond _A _nm
_atom_type_radius_contact _A _nm _pm
_atom_type_oxidation_number
_atom_type_sf_source # 'Int.Tab. Vol 2'
_atom_type_sf_Cromer_Mann_a1
_atom_type_sf_Cromer_Mann_b1
_atom_type_sf_Cromer_Mann_a2
_atom_type_sf_Cromer_Mann_b2
_atom_type_sf_Cromer_Mann_a3
_atom_type_sf_Cromer_Mann_b3
_atom_type_sf_Cromer_Mann_a4
_atom_type_sf_Cromer_Mann_b4
_atom_type_sf_Cromer_Mann_c
_atom_type_sf_dispersion_real
_atom_type_sf_dispersion_imag
_atom_type_sf_versus_angle_list # supply as text data
Atom Site data types
--------------------
_atom site label * # C12b_Asp35
_atom_site_type_symbol * # to match atom_type_symbol
_atom_site_code_1_number *
_atom_site_code_2_residue *
_atom_site_code_3_sequence *
_atom_site_code_4_remoteness *
_atom_site_code_5_chain_order *
_atom_site_code_6_alternate *
_atom_site_code_7_footnote *
_atom_site_Wyckoff_symbol *
_atom_site_description * # 'disordered'
_atom_site_calc_flag * # see Standard Codes
_atom_site_calc_attached_atom * # attached atom_site_label
_atom_site_attached_hydrogens *
_atom_site_thermal_motion_type * # see Standard Codes
_atom_site_refinement_flags * # see Standard Codes
_atom_site_constraints *
_atom_site_restraints *
_atom_site_fract_x *
_atom_site_fract_y *
_atom_site_fract_z *
_atom_site_Cartn_x * _A _nm _pm
_atom_site_Cartn_y * _A _nm _pm
_atom_site_Cartn_z * _A _nm _pm
_atom_site_U_iso_or_equiv * _A _nm _pm
_atom_site_occupancy * # must be <= 1.0
_atom_site_symmetry_multiplicity * # must be >= 1.0
_atom_site_aniso_label * # to match atom_site_label
_atom_site_aniso_U_11 * _A _nm _pm
_atom_site_aniso_U_22 * _A _nm _pm
_atom_site_aniso_U_33 * _A _nm _pm
_atom_site_aniso_U_12 * _A _nm _pm
_atom_site_aniso_U_13 * _A _nm _pm
_atom_site_aniso_U_23 * _A _nm _pm
_atom_site_fract_to_Cartn_axes # 'X//c;
_atom_site_fract_to_Cartn_mat_11
_atom_site_fract_to_Cartn_mat_21 # Matrix for transforming the
_atom_site_fract_to_Cartn_mat_31 # fractional coordinates to
_atom_site_fract_to_Cartn_mat_12 # Cartesian coordinates for
_atom_site_fract_to_Cartn_mat_22 # axial alignments given above.
_atom_site_fract_to_Cartn_mat_32 #
_atom_site_fract_to_Cartn_mat 13 # |11 12 13|
_atom_site fract_to_Cartn_mat_23 # (xyz)|21 22 23|=(x'y'z')
_atom_site_fract_to_Cartn_mat_33 # |31 32 33|
Refinement data items
---------------------
_refine_special_details
_refine_ls_structure_factor_coef # see Standard Codes
_refine_ls_matrix_type # see Standard Codes
_refine_ls_weighting_scheme # see Standard Codes
_refine_ls_hydrogen_treatment # see Standard Codes
_refine_ls_extinction procedure
_refine_ls_extinction coef
_refine_ls_abs_structure_details
_refine_ls_abs_structure_Flack
_refine_ls_abs_structure_Rogers
_refine_ls_number_reflns # reflns used in deriv (Nref)
_refine_ls_number_parameters # parameters refined (Npar)
_refine_ls_number_restraints
_refine_ls_number_constraints
_refine_ls_R_factor_all # sum(Fdif)/sum(Fcal)
_refine_ls_R_factor_obs
_refine_ls_R2_factor_all # sum(Fdif^2)/sum(Fcal^2)
_refine_ls_R2_factor_obs
_refine_ls_wR2_factor_all # sum(wFdif^2)/sum(wFcal^2)
_refine_ls_WR2_factor obs
_refine_ls_goodness_of_fit_all # sq(sum(wFdif^2)/(Nref_Npar))
_refine_ls_goodness_of_fit_obs
_refine_ls_shift/esd_max
_refine_ls_shift/esd_mean
_refine_difference_density_min _e.A _e.nm _e.pm
_refine_difference_density_max _e.A _e.nm _e.pm
Reflection data items
---------------------
_reflns_special_details
_reflns_h_min
_reflns_h_max
_reflns_k_min
_reflns_k_max
_reflns_l_min
_reflns_l_max
_reflns_number
_reflns_number_observed,
_reflns_observed criterion # '3sigma(F)'
_reflns_d_resolution_high _A _nm _pm
_reflns_d_resolution_low _A _nm
_reflns_scale_group_code *
_reflns_scale_intensity_meas *
_reflns_scale_F_squared_meas *
_reflns_scale_F_meas *
_refln_h *
_refln_k *
_refln_l *
_refln_observed_status * # see Standard Codes
_refln_refinement_status * # see Standard Codes
_refln_intensity_meas *
_refln_intensity_sigma *
_refln_intensity_calc *
_refln_F_squared_meas *
_refln_F_squared_sigma *
_refln_F_squared_calc *
_refln_F_meas *
_refln_F_sigma *
_refln_F_calc *
_refln_A_meas *
_refln_A_calc *
_refln_B_meas *
_refln_B_calc *
_refln_phase_meas * _deg _rad
_refln_phase_calc * _deg _rad
_refln_scale_group_code *
_refln_symmetry_multiplicity *
_refln_symmetry_epsilon *
_refln_sint/lambda * _A _nm _pm
_refln_wave_length * _A _nm _pm
Geometry data items
-------------------
_geom_structure_special_details
_geom_distance_atom_label_1 * # to match atom_site_label
_geom_distance_atom_label_2 * # to match atom_site_label
_geom_distance * _A _nm _pm
_geom_atom_chem_label * # chemical atom label
_geom_atom_chem_label_equiv * # to match atom_site_label
_geom_atom_chem_Cartn_x * _A _nm _pm
_geom_atom_chem_Cartn_y * _A _nm _pm
_geom_atom_chem_connections # see Standards Codes
Standard Codes Table
--------------------
atom_site_calc_flag . # determined from diffrn data
calc # calc. from geometry only
dum # a dummy atom site
atom_site_refinement_flags # the following one char flags
# are concatenated in a string
S = special position constraint on site
G = rigid group refinement of site
R = riding atom site attached to non-R
D = distance or angle restraint on site
T = thermal displacement constraints
U = Uiso or Uij restraint (rigid bond)
P = partial occupancy constraint
atom_site_thermal_motion_type aniso # anisotropic Uij
iso # isotropic U
exptl_absorpt_correction_type analyt # analytical from crystal shape
empir # empirical from measured I
refined # refined from delta-F
sphere # spherical
cylinder # cylindrical
geom_atom_chem_connect_type sing # single bond
doub # double bond
trip # triple bond
quad # quadruple bond
arom # aromatic bond
poly # polymeric bond
delo # delocalised double bond
pi # pi bond
refine_ls_matrix_type full # full matrix
atomblock # block diagonal per atom
userblock # block diagonal user_defined
diag # diagonal elements only
sparce # selected elements only
refine_structure_factor_coef Inet # net intensity
Fsqd # structure factor squared
F # structure factor
refine_ls_weighting_scheme sigma # based on measured sigmas
unit # unit weights
calc # calculated weights
refine_ls_hydrogen_treatment refall # refined all H parameters
refxyz # refined coordinates only
refU # refined U only
noref # no refinement
refln_observed_status . # observed by hkl_obs_criterion
< # unobserved " "
refln_refinement_status incl # included in ls process
excl # excluded in ls process
extn # excluded due to extinction
Please send all updates of this document to: S.R. Hall, MPI Kohlenforschung,
Kaiser Wilhelm Platz 1, D-4330 Muelheim-Ruhr, FRG. Fax:[49]208 306 407
Email: hall@mpi_muelheim.mpg.dbp.de Phone:[49]208 306 491.
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Copyright © 2005 International Union of Crystallography