International
Tables for
Crystallography
Volume G
Definition and exchange of crystallographic data
Edited by S. R. Hall and B. McMahon

International Tables for Crystallography (2006). Vol. G, ch. 3.1, pp. 77-79

Section 3.1.5.4. Data-item definitions

B. McMahona*

aInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail: bm@iucr.org

3.1.5.4. Data-item definitions

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The data blocks described in Sections 3.1.5.1[link] and 3.1.5.3[link] are used to identify the dictionary and to describe the nature and purpose of a category. The remaining data blocks in a dictionary provide the attributes of data values in a form suitable for machine extraction and validation. The following examples show how this is done for various types of data.

3.1.5.4.1. Definitions of single quantities

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Example 3.1.5.3[link] is the core dictionary definition of the data name for the ambient temperature during the experiment. Because this is a single (non-looped) value, the relevant data name is one among several discrete items in the DIFFRN category. No further description of its relationship to other data items is required.

Example 3.1.5.3. A simple definition of a data item describing a physical quantity.

[Scheme scheme5]

The type of the associated data value (numb for numerical) is specified, together with any constraint on its legal value. The range specified ( 0.0:) indicates that it may be any non-negative real number. The physical units of the quantity are also indicated.

The _definition attribute is a concise human-readable documentation of the meaning associated with the data name.

Example 3.1.5.4[link] is taken from the powder dictionary and illustrates a data item that can have only one of a limited set of values. This data item indicates the geometry of the experiment. The associated data value is of type char and may legally take only one of the two possible values listed.

Example 3.1.5.4. A data item that can take only one of a discrete set of allowed values.

[Scheme scheme7]

3.1.5.4.2. Looped data

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Many of the attributes of looped data items, such as their physical units or valid numerical values, may be defined in exactly the same way as for non-looped data. However, more care needs to be taken to describe the relationships between different looped data items.

Consider the following example listing of some three-dimensional atom-site coordinates and displacement parameters. [Scheme scheme6]

These loops, or tables of values, are properties of atom sites, each identified by a label such as O1. The definition of a data name such as _atom_site_U_iso_or_equiv expresses this by using the DDL1 _list_reference attribute (Example 3.1.5.5[link]).

Example 3.1.5.5. Definition relating a looped data item to the item used to identify a `loop packet', or row of entries in a table.

[Scheme scheme8]

For an entry in the table to make sense, the site identifier must be present, so the definition for _atom_site_label declares it a mandatory item within its list (Example 3.1.5.6[link]).

Example 3.1.5.6. Definition of a mandatory item within a loop.

[Scheme scheme9]

It is common for an atom-site identifier to be used in several related tabulations in a particular crystal structure description, and in a CIF description this means that it may occur in several different looped lists. The dictionary definition gives a formal account of this by listing the data names in other looped lists which are just different manifestations of this same item. This is done using the _list_link_child attribute, which identifies the data names to which the one being currently defined is `parent'. In Example 3.1.5.6[link] (which is a subset of the full list in the core dictionary), _atom_site_aniso_label, _geom_bond_atom_site_label_1 and _geom_bond_atom_site_label_2 are identified as children of _atom_site_label.

It can been seen immediately that _atom_site_aniso_label is the atom-site identification label appearing in the second table in the example listing above, and the _geom_bond_ items are clearly atom-site labels in a table of bonding properties between specified sites. There is, however, a difference between the two secondary tables: the bond-properties table is described by data items in the GEOM_BOND category, but the table of anisotropic displacement parameters includes data names that have the same _category attribute as the coordinate data items, namely ATOM_SITE. The latter is an example of multiple lists or tables belonging to the same category, a feature permitted only in DDL1-based data files.

3.1.5.4.3. Units

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The physical units in which a quantitative data item must be expressed are identified by the DDL1 attributes _units and _units_detail. The latter is a character field describing the units; the _units attribute is a code that may be interpreted by machine. In DDL1-based dictionaries, type codes are purely conventional, and there is no mechanism for converting units or relating quantities in different units. Table 3.1.5.1[link] lists the units codes used in the DDL1-based dictionaries described in this volume. There can be some inconsistencies: two codes (`s' and `sec') are already in use to indicate the time unit of seconds.

Table 3.1.5.1| top | pdf |
Units codes and their interpretation in DDL1-based dictionaries

Unit code ( _units)Meaning ( _units_detail)
A Ångströms
A^-1^ Reciprocal ångströms
A^2^ Ångströms squared
A^3^ Ångströms cubed
Da Daltons
K Kelvins
Kmin^-1^ Kelvins/minute
Mgm^-3^ Megagrams per cubic metre
\ms Microseconds
deg Degrees
deg/min Degrees per minute
eV Electronvolts
e_A^-3^ Electrons per cubic ångström
fm Femtometres
kPa Kilopascals
kV Kilovolts
kW Kilowatts
mA Milliamperes
min Minutes
mm Millimetres
mm^-1^ Reciprocal millimetres
s Seconds
sec Seconds

The original CIF paper (Hall et al., 1991[link]) described a convention allowing physical quantities to be listed in a CIF in units other than those specified in the dictionary. Under this convention, a data name representing a value expressed in different units could be constructed by appending one of a series of known `units extension codes' to the standard data name. Thus _cell_length_a_pm would represent a cell length expressed in picometres instead of the default ångströms. This approach is now deprecated, and all quantities must be expressed in the single unit permitted in their definition block. However, to allow the formal validation of old CIFs, a `compatibility dictionary' is available which defines all data names that could have been constructed under this convention in a properly DDL1.4-compliant form. This dictionary should only be used for validating old CIFs, and must not be used to construct new data files. The dictionary is called cif_compat.dic in the IUCr CIF dictionary register (see Section 3.1.8.2[link]).

References

Hall, S. R., Allen, F. H. & Brown, I. D. (1991). The Crystallographic Information File (CIF): a new standard archive file for crystallography. Acta Cryst. A47, 655–685.Google Scholar








































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