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. 2.5, pp. 54-55

Section 2.5.4. DDL versions

S. R. Halla* and A. P. F. Cookb

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia, and bBCI Ltd, 46 Uppergate Road, Stannington, Sheffield S6 6BX, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

2.5.4. DDL versions

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The capacity of a DDL to precisely define data items depends implicitly on the scope of the available attributes. It is quite possible, therefore, that a completely new data property cannot be specified using an existing DDL. In a field where data types evolve rapidly, the currently used dictionary language may be inadequate for the precise specification of an item. It is inevitable that future data items will exceed the capacity of existing dictionary attributes and methods to describe new data properties, and the dictionaries must evolve much in the same way that spoken languages continually adapt to changing modes of expression.

The first DDL used in crystallography (in 1990) was developed to compile a dictionary of `core structural' crystallographic data items (Hall et al., 1991[link]). These data items were intended for use when submitting a manuscript to the journal Acta Crystallographica (and still are). The `core' DDL is known commonly as DDL1 (Hall & Cook, 1995[link]). Several years later, the definition of macromolecular crystallographic data items needed hierarchical descriptors for the different levels of structural entities, and an `mmCIF' DDL, known as DDL2 (Westbrook & Hall, 1995[link]), was developed. DDL2 was used to build the mmCIF dictionary (Bourne et al., 1997[link]). DDL1 is described in this chapter and DDL2 is described in Chapter 2.6[link] . The DDL1 attributes have been used to construct the crystallographic core (fundamental structural), pd (powder diffraction), ms (modulated and composite structures) and rho (electron density) dictionaries. These dictionaries are discussed in Chapters 3.2–3.5 and presented in full in Chapters 4.1–4.4, respectively, of this volume.

It is helpful to give a brief comparison of the definition capabilities of DDL1 and DDL2. The differences may be best illustrated by simply comparing their application to the definition of the same data item. The two separate definitions of _atom_site_Cartn_x are shown in Fig. 2.5.4.1[link].

[Figure 2.5.4.1]

Figure 2.5.4.1 | top | pdf |

Comparison of DDL versions: (a) DDL1, (b) DDL2.

Although both DDL versions conform to the syntax of the STAR File (DDL1 conforms to the CIF syntax but DDL2 uses STAR File save frames not permitted in CIF data files) and are composed of similar attributes, there are clear differences. These are summarized in Table 2.5.4.1[link].

Table 2.5.4.1| top | pdf |
Comparison of DDL1 and DDL2 variants

DDL1DDL2
Data names identify the category of data as _<category>_<detail> Data names identify the category as _<category>.<detail>
   
Definitions are declared as data blocks with data_<data name> Definitions are declared starting with save_<data name> and ending with save_
   
An irreducible set of items is declared within one definition e.g. Miller indices h, k, l All items are defined in separate frames related by _item_dependent.name
   
Items that appear in lists are identified with the attribute list_ List and non-list data items are not distinguished
   
List dependencies are declared within each definition e.g. _list_reference Dependencies are declared in a category definition e.g. _category_key.name
   
  Identifies subcategories of data within category groupings e.g. matrix
   
  Provides aliases to equivalent names, including those in DDL1 dictionaries

The similarity in the two DDL versions is such that software exists for parsing and validating CIFs against the DDL1 or DDL2 dictionaries interchangeably (e.g. see the CIF toolbox software CIFtbx described in Chapter 5.4[link] ).

References

Bourne, P. E., Berman, H. M., McMahon, B., Watenpaugh, K. D., Westbrook, J. D. & Fitzgerald, P. M. D. (1997). Macromolecular Crystallographic Information File. Methods Enzymol. 277, 571–590.
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.
Hall, S. R. & Cook, A. P. F. (1995). STAR dictionary definition language: initial specification. J. Chem. Inf. Comput. Sci. 35, 819–825.
Westbrook, J. D. & Hall, S. R. (1995). A dictionary description language for macromolecular structure. http://ndbserver.rutgers.edu/mmcif/ddl/ .








































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