|
INTERNATIONAL TABLES for CRYSTALLOGRAPHY |
Volume G |
Definition and Exchange of Crystallographic Data |
This initial draft of a dictionary of data names includes textual definitions and an indication of data type, but no machine-readable attributes of the sort formalised by the dictionary definition language subsequently developed. At this stage it was still envisaged that physical quantities could be expressed in alternative units.
CIF Document: #4 Version: Oct22-89
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Contributions to the definition of data names are welcomed from all sources.
Definitions should be precise but brief. Supply an example if possible.
Note that the recognised unit attribute codes are given on the same line
as the data name, where applicable. The expected (but not mandatory) nature
of the data item is given in parentheses. Nothing in the STAR format prevents
a character item from appearing as text, or vice versa, though in many cases
this would not be sensible. Numerical data items may have the standard
deviation appended (no separating blanks) in parentheses. The Standard Codes
which are applicable to some character data items are given in Appendix 1.
DATA NAME DEFINITIONS IN ALPHABETICAL ORDER
-------------------------------------------
_atom_site GENERAL DESCRIPTION
The ator_site refers to a particular atom_type occupying a
particular position in the unit cell. A given atom_type may exist
at several atom_sites. When more than one atom_type occupies a given
position (as commonly found in many minerals) then more than one
atom_site will be defined for that position, each of the atom_sites
having the same coordinates but referring to different atom_types.
When more than one atom_site is found occupying a given position,
the sum of their atom_site_occupancy must not be greater than 1.0.
_atom_site_aniso_label (char)
This label must match one of the atom_site_label's associated with
the atomic coordinates. See atom_site_label for the definition.
_atom_site_aniso_U_11 _A _nm _pm (numb)
_atom_site_aniso_U_12 _A _nm _pm (numb)
_atom_site_aniso_U_13 _A _nm _pm (numb)
_atom_site_aniso_U_22 _A _nm _pm (numb)
_atom_site_aniso_U_23 _A _nm _pm (numb)
_atom_site_aniso_U_33 _A _nm _pm (numb)
These are the standard U(ij) components of the anisotroplc thermal
displacement parameter. The components may be entered in any order.
_atom_site_attached_hydrogens (numb)
The number of hydrogen atoms attached to the atom on this site
EXCLUDING any H atoms for which coordinates (measured or calculated)
are given. (e.g. 2 for a water O, 1 for hydroxyl O, 4 for ammonium N)
_atom_site_calc_attached_atom (char)
The atom_site_label of the atom to which a calculated atom is
attached. See definition of atom_site_label.
_atom_site_calc_flag (char)
This is a code which specifies whether the site parameters have been
calculated. '.'= not calculated; 'calc' = calculated; 'dum' = dummy
site included for compositional reasons.
_atom_site_Cartn_x _A _nm _pm (numb)
_atom_site_Cartn_y _A _nm _pm (numb)
_atom_site_Cartn_z _A _nm _pm (numb)
These are the atomic coordinates specified according to a set of
orthogonal Cartesian axes. These relationship of the these axes
to the cell axes is specified by the atom_site_fract_to_Cartn_axes
description.
_atom_site_code_1_sequence (char)
This code is used to differentiate sites containing the same
atom type, but may be used for any purpose whatsoever. The code
string may contain any alphanumeric character except a blank or
an underline '_' but the first character MUST be a digit '0-9'.
_atom_site_code_2_residue (char)
This code is intended primarily to identify specific structural
information such as the molecular fragment, amino-acid type etc.
The code should NOT contain any digit (0-9), blank or underline '_'
characters.
_atom_site_code_3_sequence (char)
This code is used to differentiate sites containing the same
residue type, but can be used for any purpose whatsoever. This
string may contain any alphanumeric character except a blank or an
underline '_' but the first character MUST be a digit '0-9'.
_atom_site_code_4_remoteness (char)
_atom_site_code_5_chain_order (char)
_atom_site_code_6_alternate (char)
_atom_site_code_7_footnote (char)
_atom_site_constraints (char)
A summary of the constraints applied to parameters at this site
(e.g. 'x=y; U11=U22'). See also atom_site_refinement_flags.
_atom_site_description (char)
A brief description of special aspects of the this site (e.g
'disordered'). See also atom_site_refinement_flags.
_atom_site_fract_to_Cartn_axes (char)
A summary of the relative alignment of the crystal cell axes
to the orthogonal axes (e.g a//x;....)
_atom_site_fract_to_Cartn_mat_11 (numb)
_atom_site_fract_to_Cartn_mat_12 (numb)
_atom_site_fract_to_Cartn_mat_13 (numb)
_atom_site_fract_to_Cartn_mat_21 (numb)
_atom_site_fract_to_Cartn_mat_22 (numb)
_atom_site_fract_to_Cartn_mat_23 (numb)
_atom_site_fract_to_Cartn_mat_31 (numb)
_atom_site_fract_to_Cartn_mat_32 (numb)
_atom_site_fract_to_Cartn_mat_33 (numb)
ts for transforming fractional coordinates to
orthogonal Cartesian coordinates. The axial alignments are
described in atom_site_fract_to_Cartn_axes.
Application of the matrix is as follows:
|11 12 13|
(xyz)|21 22 23|=(x'y'z')
|31 32 33|
_atom_site_fract_x (numb)
_atom_site_fract_y (numb)
_atom_site_fract_z (numb)
The atom site coordinates as fractions of the crystal unit cell.
_atom_site_label (char)
The atom_site_label is the unique identifier of a specific site in
the crystal structure which contains a particular atomic type, or
combination of atom types. There may be more than one label refering
to the same position in the crystal structure [This is one approach
to specifying disordered atom sites. The other, is to specify a
single site containing a mixture of atom types in a fixed proportion
defined by atom_type_description.].
****Note**** A convention for defining the atom_site_label has not
been decided on for this version of the dictionary but a labelling
scheme proposed by some package developers is given in Appendix II.
_atom_site_occupancy (numb)
Normally a number equal to one or less (1.0 is assumed if this field
is missing or defaulted). The sum of the occupancies of all the atoms
on sites that cannot be simultaneously occupied should not exceed 1.0.
However for 'dummy' atoms this number may be greater than 1.0
_atom_site_restraints (char)
Short description of restraints applied to specific parameters at
this site. These may be appears as codes in the Standard Codes Table.
See also _atom_site_refinement_flags.
_atom_site_refinement_flags (char)
A series of single letter codes which indicate that certain restraint
or constraint refinement processes were applied to this site. These
flags are listed in the Standard codes table.
_atom_site_symmetry_multiplicity (numb)
The multiplicity of a site due to the space group symmetry. This is
given in International Tables for Crystallography Vol A. Must lie
between 1 and 192.
_atom_site_thermal_motion_type (char)
The type of parameters used to describe the thermal motion of the
atom site. See Standard Codes. See also atom_site_refinement_flags.
_atom_site_type_symbol (char)
Must match a defined atom_type_symbol. Identifies the chemical
nature of the atom, or atoms, occupying this site.
_atom_site_U_iso_or_equiv _A _nm _pm (numb)
Isotropic thermal displacement parameter or equivalent isotropic
thermal displacement parameter calculated from anisotropic thermal
displacement parameters. The latter must be calculated as:
U(equiv) = 1/3 sum(j)[ sum(j){ U(ij) a*(i) a*(j) A(i).A(j) } ]
where A() are the real space vectors.
_atom_site_Wyckoff_symbol (char)
The Wyckoff symbol is as listed in the space group section of
International Tables for Crystallography Volume A.
_atom_type GENERAL DESCRIPTION
An atom_type as refers to a particular chemical species that differs
from other chemical species present in the crystal, either by being
a different chemical element, having a different oxidation state,
a different atomic scattering factor or different radius, etc. In
most compounds the different atom_types will be different chemical
elements, but the author may define atom_type in any way appropriate.
All atoms of the same atom_type are assumed to have the same chemical
properties. See also atom_type_symbol and atom_type_description.
_atom_type_description (char)
Description of the atom, or atoms, designated by this atom_type.
In most cases this will be the element name and oxidation state of
a single atom species (e.g. 'copper(II)'). In nonstoichiometric
compounds it will describe a mixture of atom types (e.g. '0.34 Iron
+ 0.66 Nickel').
_atom_type_number_in_cell (numb)
Total number of atoms of this atom_type in the full unit cell.
_atom_type_oxidation_number (numb)
Formal oxidation state of this atom_type in the crystal.
_atom_type_radius_bond _A _nm _pm (numb)
The effective intramolecular bonding RADIUS of this atom_type.
_atom_type_radius_contact _A _nm _pm (numb)
The effective intermolecular contact RADIUS of this atom_type.
_atom_type_sf_Cromer_Mann_a1 (numb)
_atom_type_sf_Cromer_Mann_a2 (numb)
_atom_type_sf_Cromer_Mann_a3 (numb)
_atom_type_sf_Cromer_Mann_a4 (numb)
_atom_type_sf_Cromer_Mann_b1 (numb)
_atom_type_sf_Cromer_Mann_b2 (numb)
_atom_type_sf_Cromer_Mann_b3 (numb)
_atom_type_sf_Cromer_Mann_b4 (numb)
_atom_type_sf_Cromer_Mann_c (numb)
The Cromer-Mann scattering factor coefficients which were used to
calculate the scattering factors for this atom_type.
_atom_type_sf_dispersion_imag (numb)
_atom_type_sf_dispersion_real (numb)
The imaginary and real components of the anomalous dispersion
scattering factors, delta f", and delta f' (in electrons) for this
atom type and radiation.
_atom_type_sf_source (char)
The reference to the scattering factors applied for this atom type.
_atom_type_sf_versus_angle_list (text)
A text list of scattering factors for different angle (or sin(theta)
on lambda) values, appropriate for this atom type.
_atom_type_symbol (char)
This symbol is used to identify the 'element' properties of the
atom_type with the atom_site that it occupies.
This character string MUST match identically one of the defined
atom_type_symbol strings, thus identifying the set of atom_type
quantities associated with this site. The type_symbol may contain any
character except a blank or an underline '_', but with the proviso
that each digit '0-9' be used only to designate an oxidation state
and as such, must be followed by a plus '+' or a minus '-' character.
It is recommended that the type_symbol be kept short (if possible 4
chars or less), and that element symbols be used when applicable.
Permissible symbols are: 'Cu', 'Cu2+', 'dummy', 'Fe3+N12+', 'S---',
'H*', 'H(SDS)' and 'kitchen.sink'.
See also atom_type GENERAL DESCRIPTION.
_cell_a _A _nm _pm (numb)
_cell_b _A _nm _pm (numb)
_cell_c _A _nm _pm (numb)
_cell_alpha _deg _rad (numb)
_cell_beta _deg _rad (numb)
_cell_gamma _deg _rad (numb)
The crystal cell lengths and angles.
_cell_formula_units_Z (numb)
The size of the formula unit is given by chemical_formula_structural
(or _moiety or _sum). The unit cell is that reported under cell_.
_cell_measurement_pressure _gPa _kPa (numb)
The pressure under which the unit cell data was measured (NOT the
pressure use to synthesize the sample).
_cell_measurement_radiation (char)
The radiation type used to measure the crystal unit cell (e.g.
'neutrons'). See also cell_measurement_wavelength.
_cell_measurement_reflns_used (numb)
The total number of reflections used to calculate the unit cell.
_cell_measurement_temperature _K _c (numb)
The temperature at which the unit cell data was measured (NOT the
temperature of synthesis).
_cell_measurement_theta_max _deg _rad (numb)
_cell_measurement_theta_min _deg _rad (numb)
The range of theta values used to measure the crystal unit cell.
_cell_measurement_wavelength _A _nm _pm (numb)
The wavelength of the radiation used for the cell measurement.
See also cell_measurement_radiation.
_cell_special_details (text)
A description of special aspects of the cell choice, noting any
possible alternate settings (e.g. 'pseudo-orthorhombic').
_cell_volume _A _nm _pm (numb)
The real space volume of the unit cell.
_chemical_compound_source (text)
Source of the compound under study, or of the parent molecule if a
simple derivative is studied. This may be the place of discovery for
minerals [from Norilsk, USSR], or the actual source of a natural
product [from the bark of Cinchona naturalis, Amazon basin, Brazil].
_chemical_formula_analytical (text)
Formula as determined by standard chemical analysis including
trace elements. Use the same format as chemical_formula_structural.
A non-stiochiometric example is: 'Fe2.45 Ni1.60 S4'.
_chemical_formula_moiety (char)
Chemical formulation in which each discrete bonded residue or ion is
given separately. Individual formulae should begin with the elements
C, H, (if present), followed by others in alphabetical order, i.e.
the Hill System used by Chemical Abstracts. The following rules apply:
* Element/count combinations should be separated one from another by one
blank space or underline character to simplify parsing.
* Charge information should be placed at the end of the residue, pre-
ceeded by a numerical multiplier if the net charge is e.g. n- or n+.
* Discrete bonded unit or ion formulations should be separated one from
another by a comma.
* Pre- or post-multipliers for individual units or ions may be needed
to conform to the stated Z-value, or to ensure charge neutrality
* Examples :
'C7 H4 Cl1 Hg1 N1 O3 S1' [a count of unity can be omitted if desired]
'C12 H17 N4 O1 S1 1+, C6 H2 N3 O7 1-'
'C12 H16 N2 O6, 5H2 O1)'
_chemical_formula_residue_seq (text)
The sequence information of the structure in terms of the amino-acid
residue codes (3-letter).
_chemical_formula_structural (char)
Chemical formulation for inorganics, organometallics, metal complexes,
in which formulations of individual bonded ligands are preserved as
discrete entities within parentheses, with post-multipliers as
required. The ligand formulations should follow the rules described for
chemical_formula_moiety in terms of element ordering, etc. Parentheses
may be nested as required. This formula should correspond to the
structure as actually reported i.e. trace elements not included under
atom_type and atom_site should not be included in this formula (see
chemical_formula_analytical). E.g. 'Ca ((Cl O3)2 O)2 (H2 O)6' and
'[Pt (N1 H3)2 (C5 H7 N3 O1)2], 2(Cl1 O4)'
_chemical_formula_sum (char)
Chemical formulation in which all discrete bonded residues and ions are
summed over the constituent elements, following the ordering as given for
chemical_formula_moiety. Example: 'C18 H19 N7 O8 S1' is the formula sum
for the second example given under chemical_formula_moiety.
_chemical_formula_weight _Dalt (numb)
Molecular weight in Daltons. This weight should correspond to the
formulation(s) given under chemical_formula_***** and, together with
the cited Z-value and cell parameters, should yield the cited density.
_chemical_melting_point _K _C (numb)
The melting point of the crystal.
_chemical_name_common
Trivial name by which compound is commonly known e.g. 1-bromoestradiol
_chemical_name_mineral (char)
Mineral name accepted by the IMA. Use only for natural minerals.
_chemical_name_structure_type (char)
Commonly used structure type name. Usually only applied to minerals
or inorganic compounds. E.g. 'perovskite', 'sphalerite' or 'A15'.
_chemical_name_systematic
IUPAC or Chemical Abstracts full name of compound under study.
(e.g. 1-bromoestra-1,3,5(10)-triene-3,17beta-diol
_computing_cell_refinement (char)
Software used to establish the cell choice, and estimate the cell
dimensions. See also cell_measurement_ parameters. Give software
name and brief reference (e.g. 'CELDIM (Davis)').
_computing_data_collection (char)
Software used to measure the raw intensity data (e.g. 'CAD4 (Enraf
Nonius)').
_computing_data_reduction (char)
Software used to process the raw diffraction data and reduce it to
a unique set of structure factor data (e.g. 'DIFDAT,SORTRF,ADDREF
(XTAL3.0)').
_computing_diagram_preparation (char)
Software used to prepare diagrams for publication (e.g. 'ORTEP
(Johnson)').
_computing_molecular_graphics (char)
Software used to display the crystal structure during the analysis
(e.g. FRODO (Jones)').
_computing structure refinement (char)
Software used to refine the structural parameters (e.g. 'CRYSTALS
(Watkin)').
_computing_structure_solution (char)
Software used to determine the initial model of the structure (e.g.
'SHELX (Sheldrick)').
_data_base_code_CAS (char)
_data_base_code_CSD (char)
_data_base_code_ICSD (char)
_data_base_code_MDF (char)
_data_base_code_NBS (char)
_data_base_code_PDF (char)
_diffrn_attenuator_number (char)
_diffrn_attenuator_scale (numb)
_diffrn_camera_geometry (char)
_diffrn_camera_model (char)
_diffrn_diffractometer_geometry (char)
_diffrn_diffractometer_model (char)
_diffrn_measurement_process (char)
_diffrn_orient_matrix_11 (numb)
_diffrn_orient_matrix_12 (numb)
_diffrn_orient_matrix_13 (numb)
_diffrn_orient_matrix_21 (numb)
_diffrn_orient_matrix_22 (numb)
_diffrn_orient_matrix_23 (numb)
_diffrn_orient_matrix_31 (numb)
_diffrn_orient_matrix_32 (numb)
_diffrn_orient_matrix_33 (numb)
_diffrn_orient_refln_chi _deg _rad (numb)
_diffrn_orient_refln_h (numb)
_diffrn_orient_refln_k (numb)
_diffrn_orient_refln_l (numb)
_diffrn_orient_refln_kappa _deg _rad (numb)
_diffrn_orient_refln_phi _deg _rad (numb)
_diffrn_orient_refln_psi _deg _rad (numb)
_diffrn_pressure _gPa _kPa (numb)
_diffrn_radiation_detector (char)
_diffrn_radiation_monochromator (char)
_diffrn_radiation_source (char)
_diffrn_radiation_type (char)
_diffrn_radiation_wavelength _A _nm _pm (numb)
_diffrn_refln_attenuator_code (numb)
_diffrn_refln_chi _deg _rad (numb)
_diffrn_refln_counts_bg_1 (numb)
_diffrn_refln_counts_bg_2 (numb)
_diffrn_refln_counts_net (numb)
_diffrn_refln_counts_peak (numb)
_diffrn_refln_counts_total (numb)
_diffrn_refln_h (numb)
_diffrn_refln_k (numb)
_diffrn_refln_l (numb)
_diffrn_refln_intensity (numb)
_diffrn_refln_intensity_sigma (numb)
_diffrn_refln_kappa _deg _rad (numb)
_diffrn_refln_omega _deg _rad (numb)
_diffrn_refln_phi _deg _rad (numb)
_diffrn_refln_psi _deg _rad (numb)
_diffrn_refln_scale_group_code (numb)
_diffrn_refln_Sint/lambda _A _nm _pm (numb)
_diffrn_refln_theta _deg _rad (numb)
_diffrn_reflns_h_max (numb)
_diffrn_reflns_h_min (numb)
_diffrn_reflns_k_max (numb)
_diffrn_reflns_k_min (numb)
_diffrn_reflns_l_max (numb)
_diffrn_reflns_l_min (numb)
_diffrn_reflns_merge_R_factor (numb)
_diffrn_reflns_number (numb)
_diffrn_reflns_reduction_process (text)
_diffrn_reflns_theta_max _deg _rad (numb)
_diffrn_reflns_theta_min _deg _rad (numb)
_diffrn_reflns_transf_matrix_11 (numb)
_diffrn_reflns_transf_matrix_12 (numb)
_diffrn_reflns_transf_matrix_13 (numb)
_diffrn_reflns_transf_matrix_21 (numb)
_diffrn_reflns_transf_matrix_22 (numb)
_diffrn_reflns_transf_matrix_23 (numb)
_diffrn_reflns_transf_matrix_31 (numb)
_diffrn_reflns_transf_matrix_32 (numb)
_diffrn_reflns_transf_matrix_33 (numb)
_diffrn_scale_I_net (numb)
_diffrn_scale_group_code (numb)
_diffrn_special_details (text)
_diffrn_standards_h (numb)
_diffrn_standards_k (numb)
_diffrn_standards_l (numb)
_diffrn_standards_decay_% (numb)
_diffrn_standards_interval _refn _hour _min _sec (numb)
_diffrn_standards_number (numb)
_diffrn_standards_scale_sigma (numb)
_diffrn_temperature _K _C (numb)
_exptl_absorpt_coefficient_mu _mm _cm (numb)
The absorption coefficient mu calculated from atomic content of
the cell, the density and the radiation.
_exptl_absorpt_correction_T_max (numb)
_exptl_absorpt_correction_T_min (numb)
The maximum and minimum T(bar) values for the crystal used.
_exptl_absorpt_correction_type (char)
The absorption correction description. Use the Standard Codes or
the name and reference of the computer program applied.
_exptl_crystal_F(000) (numb)
The estimated number of electrons in the crystal unit cell.
_exptl_crystal_colour (char)
The colour of the crystal (e.g. 'dark green').
_exptl_crystal_density_diffrn _g.cm _Mg.m _kg.m (numb)
_exptl_crystal_density_measured _g.cm _Mg.m _kg.m (numb)
These densities are the calculated (from crystal cell and contents)
and measured (using standard chemical and physical methods) values.
_exptl_crystal_description (text)
Provides a brief description of the crystal quality and habit.
Dimensional information can be included but this is better placed
in the crystal_face parameters.
_exptl_crystal_face_diffr_chi _deg _rad (numb)
_exptl_crystal_face_diffr_kappa _deg _rad (numb)
_exptl_crystal_face_diffr_phi _deg _rad (numb)
_exptl_crystal_face_diffr_psi _deg _rad (numb)
The diffractometer angle settings for a specific crystal face that
is identified by the face_h _k _l indices.
_exptl_crystal_face_h (numb)
_exptl_crystal_face_k (numb)
_exptl_crystal_face_l (numb)
The Miller indices assigned to a specific crystal face.
_exptl_crystal_face_perp_dist _mm _cm (numb)
The perpendicular distance of a face to centre of the crystal.
_exptl_crystal_size_max _mm _cm (numb)
_exptl_crystal_size_mid _mm _cm (numb)
_exptl_crystal_size_min _mm _cm (numb)
The maximum, medial and minimum dimensions of the crystal.
_exptl_special_details (text)
Any special information about the crystal growing or the preparation
of the crystal for the diffraction measurement (e.g. 'crystal
mounted in a Argon-filled quartz capillary').
_geom_atom_chem_Cartn_x _A _nm _pm (numb)
_geom_atom_chem_Cartn_y _A _nm _pm (numb)
The Cartesian coordinates x and y of the projected chemical diagram
for a specific atom site identified by chem_label and site_label.
_geom_atom_chem_connections (text)
The list of other chem_label's that the atom site identified by
this chem_label is connected to (e.g. 'C5 O3').
_geom_atom_chem_label (char)
_geom_atom_site_label (char)
The chem_label is the unique chemical identification code for this
atom site. The site_label is the crystallographic label for the
same atom site (this must match identically with one of the
atom_site_label's in the atom_site_list.
_geom_distance _A _nm _pm (numb)
_geom_distance_atom_label_1 (char)
_geom_distance_atom_label_2 (char)
The geom_atom_site_labels of the two atoms in the asymmetric unit
that define the distance. Distances related by symmetry should not
be included. This data is used primarlly for checking the accuracy
of the atom_site coordinate data.
_geom_structure_special_details (text)
This provides for special structural details to be noted (e.g.
'Note that the phenyl group in molecule B is disordered.').
_journal_coden_ASTM (char)
_journal_coden_Cambridge (char)
_journal_coeditor_address (text)
_journal_coeditor_code (char)
_journal_coeditor_email (char)
_journal_coeditor_fax (char)
_journal_coeditor_name (char)
_journal_coeditor_notes (text)
_journal_coeditor_phone (char)
_journal_date_accepted (char)
_journal_date_from_coeditor (char)
_journal_date_printers_final (char)
_journal_date_printers_first (char)
_journal_date_proofs_in (char)
_journal_date_proofs_out (char)
_journal_date_recd_copyright (char)
_journal_date_recd_electronic (char)
_journal_date_recd_hard_copy (char)
_journal_date_to_coeditor (char)
_journal_issue (char)
_journal_name_full (char)
_journal_page_first (char)
_journal_page_last (char)
_journal_suppl_publ_number (char)
_journal_suppl_publ_pages (numb)
_journal_techeditor_address (text)
_journal_techeditor_code (char)
_journal_techeditor_email (char)
_journal_techeditor_fax (char)
_journal_techeditor_name (char)
_journal_techeditor_notes (text)
_journal_techeditor_phone (char)
_journal_volume (char)
_journal_year (char)
_publ_abstract (text)
_publ_acknowledgements (text)
_publ_author_address (text)
The address of the author named in _publ_author_address.
_publ_author_name (char)
A single authors name of publication data. The family name, followed
by a comma, precedes the first names or initials. E.g. "O'Neil, F.K."
_publ_contact_author_address (text)
The name and address of the author to be contacted by the journal
and editorial staff.
_publ_contact_author_email (char)
_publ_contact_author_fax (char)
_publ_contact_author_phone (char)
_publ_contact_letter (text)
Leteer accompanying the submitted data and manuscript.
_publ_discussion (text)
_publ_experimental (text)
_publ_figure_captions (text)
_publ_introduction (text)
_publ_manuscript (text)
_publ_references (text)
_publ_related_literature (text)
_publ_requested_coeditor_name (char)
_publ_requested_journal (char)
_publ_table_legends (text)
_publ_title (text)
_refine_difference_density_max _e.A _e.nm _e.pm (numb)
_refine_difference_density_min _e.A _e.nm _e.pm (numb)
The largest and smallest density values in the final difference
Fourier map.
_refine_ls_R2_factor_all (numb)
_refine_ls_R2_factor_obs (numb)
The R(squared) agreement factor for all reflection data, and for
reflection data considered to be observed (see _reflns_observed_
criterion). This factor is defined to be ratio of the reflection
sums of (Fdif)squared to (Fcal)squared.
_refine_ls_R_factor_all (numb)
_refine_ls_R_factor_obs (numb)
The R agreement factor for all reflection data, and for reflection
data considered to be observed (see _reflns_observed_criterion).
This factor is defined to be ratio of the reflection sums of Fdif
to Fcal.
_refine_ls_abs_structure_Flack (numb)
This measure of absolute structure (enantiomorph or polarity) is
defined in the paper by H.D. Flack (1983) Acta Cryst. A39, 876.
The value must be between 0. and 1. with a standard deviation.
_refine_ls_abs structure_Rogers (numb)
This measure of absolute structure (enantiomorph or polarity) is
defined in the paper by D. Rogers (1981) Acta Cryst. A37, 734.
_refine_ls_abs_structure_description (text)
Information about the nature of the absolute structure determination.
_refine_ls_extinction_coefficient (numb)
The extinction coefficient applied to the structure factor data. The
nature of the extinction coefficient is described in
_refine_ls_extinction_procedure.
_refine_ls_extinction_procedure (char)
A description of the extinction process applied to the data, and the
precise nature of _refine_ls_extinction_coefficient.
_refine_ls_goodness_of_fit_all (numb)
_refine_ls_goodness_of_fit_obs (numb)
The Goodness-of_fit parameters for all data and observed data after
the final cycle of least squares. This parameter is sometimes referred
to as the 'reduced Chi Square' term and is defined as square root of
the ratio of the reflection sum of w(Fdiff)squared to the difference
between the number of reflections used in the least squares and the
number of parameters refined. See _refine_ls_number_parameters and
_refine_ls_number_reflns. Some account should also be taken of any
parameters restrained in the least squares process.
_refine_ls_hydrogen_treatment (char)
The treatment of hydrogen atoms in the least squares refinement
should be indicated, either with one of the Standard Codes or a
short description.
_refine_ls_matrix_type (char)
The type of matrix or matrices used to accumulate the least squares
derivatives. Use the Standard Codes or a short description.
_refine_ls_number_constraints (numb)
The number of constrained (non-refined or dependent) variables in
the least squares process. These may be due to symmetry or any other
constraint process (e.g. rigid-body refinement).
_refine_ls_number_parameters (numb)
The total number of parameters refined in the least squares process.
_refine_ls_number_reflns (numb)
The total number of reflections which contributed to the least
squares derivatives.
_refine_ls_number_restraints (numb)
The number of restrained variables. ***Note that this data item
requires further definition.
_refine_ls_structure_factor_coef (char)
The structure factor coefficient used in the least squares process.
Use one of the Standard Codes or a short description.
_refine_ls_shift/esd_max (numb)
_refine_ls_Shift/esd_mean (numb)
The largest and the smallest ratios of the final least squares
shift of any parameter over the final estimated standard deviation.
_refine_ls_wR2_factor_all (numb)
_refine_ls_wR2_factor_obs (numb)
The weighted R(squared) agreement factor for all reflection data,
and for reflection data considered to be observed (see _reflns_
observed_criterion). This factor is defined to be ratio of the
reflection sums of w(Fdif)squared to w(Fcal)squared.
_refine_ls_weighting_scheme (char)
The weighting scheme applied in the least squares process. Use a
Standard Code or a short description.
_refine_special_details (text)
A description of any aspect of the refinement process that warrants
special mention.
_refln_A_calc (numb)
_refln_A_meas (numb)
_refln_B_calc (numb)
_refln_B_meas (numb)
The calculated, measured structure factor components [A is
/F/cos(phase); B is /F/sin(phase)], in electrons.
_refln_F_calc (numb)
_refln_F_meas (numb)
_refln_F_sigma (numb)
The calculated, measured and standard deviation (derived from
measured data) of the structure factors, in electrons.
-refln_F_squared_calc (numb)
-refln_F_squared_meas (numb)
-refln_F_squared_sigma (numb)
The calculated, measured and standard deviation (derived from
measured data) of the squared structure factors, in electrons
squared.
_refln_h (numb)
_refln_k (numb)
_refln_l (numb)
The Miller indices of the reflections used to determine the
reported structural parameters.
_refln_intensity_calc (numb)
_refln_intensity_meas (numb)
_refln_intensity_sigma (numb)
The calculated, measured and standard deviation (derived from
measured data) of the intensity, in the measured units.
_refln_observed_status (char)
The code indicating whether the reflection is 'observed' or
'unobserved' according to the _reflns_observed_criterion. The
frequently used codes are listed in the Standard Codes Table.
_refln_phase_calc _deg _rad (numb)
_refln_phase_meas _deg _rad (numb)
The structure factor phase.
_refln_refinement_status (char)
The code indicating how a reflection was treated in the structure
refinement process. See the Standard Codes Table.
_refln_scale_group_code (char)
The scale group code when different parts of the reflection data
have different scales. These will correspond to the codes defined
in _reflns_scale_group_code.
_refln_sint/lambda _A _nm _pm (numb)
sine(theta) divided by the wavelength.
_refln_symmetry_epsilon (numb)
The symmetry reinforcement factor corresponding to the number of
times the reflection indices are generated identically from the
symmetry operations for the space group.
_refln_symmetry_multiplicity (numb)
The number of equivalent reflections. This is the number of
reflections which are expected to have the same structure factor
value from the symmetry and the Friedel relationship.
_reflns_d_resolution_high _A _nm _pm (numb)
_reflns_d_resolution_low _A _nm _pm (numb)
These are the highest resolution (lowest interplanar d value) and
lowest resolution (largest d value) reflection present in the data.
_reflns_h_max (numb)
_reflns_h_min (numb)
_reflns_k_max (numb)
_reflns_k_min (numb)
_reflns_l_max (numb)
_reflns_l_min (numb)
The maximum and minimum Miller indices for the reflection data used
in the structure determination process. Note that these may not be
same as the limits for the raw diffraction data (see _diffrn_reflns).
_reflns_number (numb)
This is the total number of reflections in the reflection list (see
_refln_h etc.). This is may contain Friedet equivalent reflections
according to the nature of the structure and the procedures used.
The text item _reflns_special_details should provide details about
the nature of the reflection list and its contents.
_reflns_number_observed (numb)
The number of reflections in the reflection list which satisfy the
'observed' condition specified in _reflns_observed_criterion.
_reflns_observed_criterion (char)
The condition by which a reflection is considered to be 'observed'.
This criterion for observability is usually expressed in terms of
the standard deviation of a structure factor related term (e.g.
'>2sigma(I)').
_reflns_scale_group_code (char)
This is the code that identifies the scales that accompany it in
the scale list. These scales are refined quantities and may not
correspond to those associated with _diffrn_scale_group_code.
_reflns_scale_intensity_meas (numb)
The scale applied to all measured intensities associated with this
scale group code.
_reflns_scale_F_squared_meas (numb)
The scale applied to all measured structure factor squared values
associated with this scale group code.
_reflns_scale_F_meas (numb)
The scale applied to all measured structure factor values associated
with this scale group code.
_reflns_special_details (text)
information about the reflection data not covered by the other
-reflns_ data names. This should include details of the Friedel
related reflection data, and how this is identified.
_symmetry_crystal_axes (char)
This specifies the crystal axes choice: 'triclinic', 'monoclinic',
'orthorhombic', 'hexagonal', rhombohedral' and 'cubic'.
_symmetry_equiv_pos_as_xyz (char)
The symmetrically equivalent positions due to space group symmetry
in Jones Faithful representation. Use as given in International
Tables for Crystallography Volume A. All equivalent position should
be entered, including those for a centred lattice. Each string of
characters should be bounded by quotes (e.g. '-y+x,-y,1/3+z'). Note
that except for space group P1 this will be a looped data item.
_symmetry_name_Hall (char)
As defined by S.R.Hall Acta Cryst. (1981) A37, 517. This symbol gives
the setting explicitly. Leave spaces between the separate components
of the symbol (e.g. '-F 2 2').
_symmetry_name_Hermann-Mauguin (char)
Use the FULL symbol given in International Tables for Crystallography
Vol A to indicate setting. Leave spaces between symbols refering to
different axes (e.g. 'P 21 21 21'). Unless indicated elsewhere the
centrosymmetric setting will be assumed. Note that this symbol is not
always unique to the setting used in contrast to symmetry_name_Hall.
_symmetry_name_Int_Tables_number (numb)
The space group number from International Tables for Crystallography
Vol A.
Appendix 1: 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
Appendix II: Atom Labelling Proposal
------------------------------------
An atom labelling schem has not been yet agreed upon for CIF. What follows
here is a proposal based upon the CIF atom site codes listed above. The
adoption of a simple but flexible label, involving the atom_site_type_symbol
and the atom_site_codes 1 to 3, by a number of software developers is described
below.
The atom_site_label is the unique identifier of a specific site in the crystal
structure which contains a particular atomic type, or combination of atom types.
There may be more than one atom_site_label refering to the same position in the
crystal structure [This is one approach to specifying disordered atom sites.
The other, is to specify a single site containing a mixture of atom types in a
fixed proportion defined by atom_type_description.].
The nature of the atom, or atoms, at each site is uniquely specified by the
atom_site_type_symbol. This symbol is the first, and the only mandatory, item
in the atom_site_label. It points to the set of 'atom_type_' data items which
specify all of the information about the atom, or atoms, at this site. The
atom_site_type_symbol is referred to as the "root" or "zero-order" component
of the atom_site_label because it must always be present in the label. The
other optional components of the atom_site_label are items named with the
prefix 'atom_site_code_'. Site_codes need only be included in the
atom_site_label to ensure that it is unique. The site_codes are added to the
atom_site_label (from left to right) in the order designated by the 'N' in
the site_code_N. The rules for concatenation, and the definition of the
component quantities, are given below. Note that the underline character '_'
may only be used in a label as a component separator.
The proposed structure of the atom_site_label is, in addition to being flexible
and visually decipherable, particularly well suited to computer applications.
The separate site_code components can be easily identified and stripped with a
single pass, from left to right, along the label string. Note that the underline
separators are only used if higher order components exist. If intermediate
components are not used they may be omitted provided the underline separators
are inserted. For example the label 'C233__ggg' is acceptable and indicates that
components 2 and 3 were not used. There is no requirement that the same number
of site_codes be used in each label (e.g. one site_label may contain only the
type_symbol while another contains site_codes up to 7). Note that site_codes
not present in a label will, on stripping, be assumed blank.
Components of atom_site_label
-----------------------------
Component 0: atom_site_type_symbol (mandatory)
This character string MUST match identically one of the defined
atom_type_symbol strings, thus identifying the set of atom_type
quantities associated with this site. The type_symbol may contain
any character except a blank or an underline '_', but with the
proviso that each digit '0-9' be used only to designate an
oxidation state and as such, must be followed by a plus '+' or
a minus '-' character. It is recommended that the type_symbol
be kept short (if possible 4 chars or less), and that element
symbols be used when applicable. Permissible labels based on
this component alone are: 'Cu', 'Cu2+', 'dummy', 'Fe3+Ni2+',
'S---', 'H*', 'H(SDS)' and 'kitchen.sink'.
Component 1: atom_site_code_1_sequence (optional)
This string may contain any alphanumeric character except a
blank or an underline '_' but the first character MUST be a
digit '0-9'. it is intended primarily to differentiate sites
containing the same atom type, but can be used for any purpose
whatsoever. This string is concatenated directly with the
atom_site_type_symbol. Examples of permissible labels are:
'C1', 'C103g28', 'Fe3+17b', 'H*251' and 'boron2a'.
Separator: An underline '_' character must be inserted as a separator if
any components beyond 1 are included in the label.
Component 2: atom_site_code_2_residue (optional)
This string MUST NOT contain any digit (0-9), blank or underline
'_' characters. It is intended primarily to identify specific
structural information such as the molecular fragment, amino-acid
type and so on. This string is separated from the code_1_sequence,
or if this not present, the type_symbol, by an underline
character.
Component 3: atom_site_code_3_sequence (optional)
This string may contain any alphanumeric character except a
blank or an underline '_' but the first character MUST be a
digit '0-9'. It is intended primarily to differentiate sites
containing the same residue type, but can be used for any
purpose whatsoever. This string is concatenated directly with
the atom_site_code_2_residue. Examples of permissible labels
are: 'C1g1_asp22', Fe3+2_cell665' and 'Ca_mol2'.
Separator: An underline '_' character must be inserted as a separator if
any components beyond 3 are included in the label.
The remaining atom_site_codes (4 to 7) have not been defined within the label
but are assumed to separated by underlines as above.
--------------------------------
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: [email protected] Phone:[49]208 306 491.
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Copyright © 2005 International Union of Crystallography