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International
Tables for Crystallography Volume G Definition and exchange of crystallographic data Edited by S. R. Hall and B. McMahon © International Union of Crystallography 2006 |
International Tables for Crystallography (2006). Vol. G. ch. 5.5, p. 539
Section 5.5.2.1. PDB format
a
Protein Data Bank, Research Collaboratory for Structural Bioinformatics, Rutgers, The State University of New Jersey, Department of Chemistry and Chemical Biology, 610 Taylor Road, Piscataway, NJ 08854-8087, USA |
For the past 30 years, the PDB has served as the single central repository for macromolecular structure data. The data format used to store archival entries in the PDB is a column-oriented data format resembling many data formats developed to accommodate the limitations of paper punched-card technology (see Chapter 1.1![[link]](/graphics/greenarr.gif)
). An example of the data format is shown in Fig. 5.5.2.1.
![[Figure 5.5.2.1]](/figures/Gafig5o5o2o1thm.gif)
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Excerpt of records from a PDB data file. |
Many of the data records in this format are prefixed with a record tag (e.g. CRYST1, ATOM) followed by individual items of data. The specifications for the records in this data format are described informally by Callaway et al. (1996). In addition to the labelled records as in Fig. 5.5.2.1, many data records in the PDB format are presented as unstructured or only semi-structured remark records.
References
Callaway, J., Cummings, M., Deroski, B., Esposito, P., Forman, A., Langdon, P., Libeson, M., McCarthy, J., Sikora, J., Xue, D., Abola, E., Bernstein, F., Manning, N., Shea, R., Stampf, D. & Sussman, J. (1996). Protein Data Bank contents guide: Atomic coordinate entry format description. Brookhaven National Laboratory, New York, USA. Available from http://www.wwpdb.org/documentation/PDB_format_1996.pdf
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