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. 5.1, pp. 483-484

Section 5.1.3.1. 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: yaya@bernstein-plus-sons.com

5.1.3.1. 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. 5.1.3.1[link] and 5.1.3.2[link]). If the need is to extract mmCIF data from the output of a major application, the PDB provides PDB_EXTRACT (http://sw-tools.pdb.org/apps/PDB_EXTRACT/ ).

[Figure 5.1.3.1]

Figure 5.1.3.1 | top | pdf |

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

[Figure 5.1.3.2]

Figure 5.1.3.2 | top | pdf |

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. 5.1.3.3[link]).

[Figure 5.1.3.3]

Figure 5.1.3.3 | top | pdf |

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 (ftp://ftp.iucr.org/pub/ciftex.tar.Z ) (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 (http://www.chem.gla.ac.uk/~louis/software/utils/ ), 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 (http://sw-tools.pdb.org/apps/CIFTr/ ) to translate from the extended mmCIF format described in Appendix 3.6.2[link] to PDB format and MAXIT (http://sw-tools.pdb.org/apps/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.

References

Bernstein, F. C. & Bernstein, H. J. (1996). Translating mmCIF data into PDB entries. Acta Cryst. A52 (Suppl.), C-576.
Bernstein, H. J. (1997). cif2cif – CIF copy program. Bernstein + Sons, Bellport, NY, USA. Included in http://www.bernstein-plus-sons.com/software/ciftbx .
Bernstein, H. J. & Bernstein, F. C. (2002). YAXDF and the interaction between CIF and XML. Acta Cryst. A58 (Suppl.), C257.
Bernstein, 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 http://www.bernstein-plus-sons.com/software/pdb2cif .
Flack, H. D., Blanc, E. & Schwarzenbach, D. (1992). DIFRAC, single-crystal diffractometer output-conversion software. J. Appl. Cryst. 25, 455–459.
Hall, S. R. & Sievers, R. (1993). CIF applications. I. QUASAR: for extracting data from a CIF. J. Appl. Cryst. 26, 469–473.
Stampf, D. R. (1994). ZINC – galvanizing CIF to work with UNIX. Manual. Protein Data Bank, Brookhaven National Laboratory, USA.
Walters, P. & Stahl, M. (1994). BABEL reference manual. Version 1.06. Dolata Research Group, Department of Chemistry, University of Arizona, USA.








































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