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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. 5.1, pp. 483-484
Section 5.1.3.1. Working with filter utilities
a
Department of Mathematics and Computer Science, Kramer Science Center, Dowling College, Idle Hour Blvd, Oakdale, NY 11769, USA |
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]](/graphics/greenarr.gif)
). Babel includes conversions to and from PDB format. Therefore, by the use of cif2pdb (Bernstein & Bernstein, 1996) and pdb2cif (Bernstein et al., 1998) combined with Babel, many macromolecular applications can be made CIF-aware without changing their code (see Figs. 5.1.3.1 and 5.1.3.2). 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]](/figures/Gafig5o1o3o1thm.gif)
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Example of using filters to make a PDB-aware application CIF-aware. |
![[Figure 5.1.3.2]](/figures/Gafig5o1o3o2thm.gif)
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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) or cif2cif (Bernstein, 1997), which accept request lists specifying the order in which data are to be presented (see Fig. 5.1.3.3).
![[Figure 5.1.3.3]](/figures/Gafig5o1o3o3thm.gif)
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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 (ftp://ftp.iucr.org/pub/ciftex.tar.Z
) (to convert from CIF to ![[\hbox{\TeX}]](/teximages/abpre6/abpre6fi2.svg)
) and ZINC (Stampf, 1994) (to unroll CIFs for use by Unix utilities)] are discussed in Chapter 5.3
. 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) to translate many diffractometer output formats to CIF. The program cif2xml (Bernstein & Bernstein, 2002) 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
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
for an extended discussion of the handling of mmCIF in the PDB software environment.
References
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