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

International Tables for Crystallography (2006). Vol. G. ch. 5.1, pp. 483-484

Section Working with filter utilities

H. J. Bernsteina*

aDepartment of Mathematics and Computer Science, Kramer Science Center, Dowling College, Idle Hour Blvd, Oakdale, NY 11769, USA
Correspondence e-mail: Working with filter utilities

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One solution to making an existing application aware of a new data format is to leave the application unchanged and change the data instead. For almost all crystallographic formats other than CIF, the Swiss-army knife of conversion utilities is Babel (Walters & Stahl, 1994[link]). Babel includes conversions to and from PDB format. Therefore, by the use of cif2pdb (Bernstein & Bernstein, 1996[link]) and pdb2cif (Bernstein et al., 1998[link]) combined with Babel, many macromolecular applications can be made CIF-aware without changing their code (see Figs.[link] and[link]). If the need is to extract mmCIF data from the output of a major application, the PDB provides PDB_EXTRACT ( ).


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Example of using filters to make a PDB-aware application CIF-aware.


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Example of using filters to make a general application CIF-aware.

Creating a filter program to go from almost any small-molecule format to core CIF is easy. In many cases one need only insert the appropriate `loop_' headers. Creating a filter to go from CIF to a particular small-molecule format can be more challenging, because a CIF may have its data in any order. This can be resolved by use of QUASAR (Hall & Sievers, 1993[link]) or cif2cif (Bernstein, 1997[link]), which accept request lists specifying the order in which data are to be presented (see Fig.[link]).


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Using QUASAR or cif2cif to reorder CIF data for an order-dependent application or filter.

There are a significant and growing number of filter programs available. Several of them [QUASAR, cif2cif, ciftex ( ) (to convert from CIF to [\hbox{\TeX}]) and ZINC (Stampf, 1994[link]) (to unroll CIFs for use by Unix utilities)] are discussed in Chapter 5.3[link] . In addition there are CIF2SX by Louis J. Farrugia ( ), to convert from CIF to SHELXL format, and DIFRAC (Flack et al., 1992[link]) to translate many diffractometer output formats to CIF. The program cif2xml (Bernstein & Bernstein, 2002[link]) translates from CIF to XML and CML. The PDB provides CIFTr by Zukang Feng and John Westbrook ( ) to translate from the extended mmCIF format described in Appendix 3.6.2[link] to PDB format and MAXIT ( ), a more general package that includes conversion capabilities. See also Chapter 5.5[link] for an extended discussion of the handling of mmCIF in the PDB software environment.


First citationBernstein, F. C. & Bernstein, H. J. (1996). Translating mmCIF data into PDB entries. Acta Cryst. A52 (Suppl.), C-576. Google Scholar
First citationBernstein, H. J. (1997). cif2cif – CIF copy program. Bernstein + Sons, Bellport, NY, USA. Included in . Google Scholar
First citationBernstein, H. J. & Bernstein, F. C. (2002). YAXDF and the interaction between CIF and XML. Acta Cryst. A58 (Suppl.), C257.Google Scholar
First citationBernstein, H. J., Bernstein, F. C. & Bourne, P. E. (1998). CIF applications. VIII. pdb2cif: translating PDB entries into mmCIF format. J. Appl. Cryst. 31, 282–295. Software available from .Google Scholar
First citationFlack, H. D., Blanc, E. & Schwarzenbach, D. (1992). DIFRAC, single-crystal diffractometer output-conversion software. J. Appl. Cryst. 25, 455–459.Google Scholar
First citationHall, S. R. & Sievers, R. (1993). CIF applications. I. QUASAR: for extracting data from a CIF. J. Appl. Cryst. 26, 469–473.Google Scholar
First citationStampf, D. R. (1994). ZINC – galvanizing CIF to work with UNIX. Manual. Protein Data Bank, Brookhaven National Laboratory, USA.Google Scholar
First citationWalters, P. & Stahl, M. (1994). BABEL reference manual. Version 1.06. Dolata Research Group, Department of Chemistry, University of Arizona, USA.Google Scholar

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