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. 1.1, p. 3

Section 1.1.3. Card-image formats

S. R. Halla* and B. McMahonb

aSchool of Biomedical and Chemical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia, and bInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail:  syd@crystal.uwa.edu.au

1.1.3. Card-image formats

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Although the interchange of scientific information depends implicitly on an agreed data format, it remains independent of whether the transmission medium is paper tape, punched card, magnetic tape, computer chip or the Internet. Crystallography has employed countless data-exchange approaches and formats over the past 60 years. Prior to the advent of computers, the standard approach involved the exchange of typed tables of coordinates and structure factors with descriptive headers. In the 1950s and 1960s, as computers became the dominant generators of data, the transfer of data between laboratories was still relatively uncommon. When it was necessary, the Hollerith card formats of commonly used programs, such as ORFLS (Busing et al., 1962[link]) and XRAY (Stewart, 1963[link]), usually sufficed. Even when magnetic tape drives became common and were standardized (mainly to the 1/2-inch 2400-foot reel), the 80-column `card-image' formats of these programs remained the most popular data exchange and deposition approach.

As the storage and transporting of electronic data became easier and cheaper, structural information was increasingly deposited directly in databases such as the Cambridge Structural Database (CSD; Allen, 2002[link]) and the Protein Data Bank (PDB; Bernstein et al., 1977[link]). The CSD and PDB simplified these depositions by using standard layouts such as the ASER, BCCAB and PDB formats. Both the PDB and CSD used, and indeed still use as a backup deposition mode, fixed formats with 80-character records and identifier codes. Examples of these format styles are shown in Figs. 1.1.3.1[link] and 1.1.3.2[link].

[Figure 1.1.3.1]

Figure 1.1.3.1 | top | pdf |

An abbreviated example of a PDB format file.

[Figure 1.1.3.2]

Figure 1.1.3.2 | top | pdf |

An example of a CSD BCCAB format file.

The card-image approach, involving a rigid preordained syntax, survived for more than two decades because it was simple, and the suite of data types used to describe crystal structures remained relatively static.

References

Allen, F. H. (2002). The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Cryst. B58, 380–388.
Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol. 112, 535–542.
Busing, W. R., Martin, K. O. & Levy, H. A. (1962). ORFLS. Report ORNL-TM-305. Oak Ridge National Laboratory, Tennessee, USA.
Stewart, J. (1963). XRAY63 Crystal Structure Calculations System. Report TR-64–6 (NSG-398). Computer Science Center, University of Maryland, USA, and Research Computer Center, University of Washington, USA.








































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