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. 5.3, pp. 499-525
doi: 10.1107/97809553602060000753

Chapter 5.3. Syntactic utilities for CIF

B. McMahona*

aInternational Union of Crystallography, 5 Abbey Square, Chester CH1 2HU, England
Correspondence e-mail: bm@iucr.org

References

Allen, F. H. (2002). The Cambridge Structural Database: a quarter of a million crystal structures and rising. Acta Cryst. B58, 380–388.
Allen, F. H., Johnson, O., Shields, G. P., Smith, B. R. & Towler, M. (2004). CIF applications. XV. enCIFer: a program for viewing, editing and visualizing CIFs. J. Appl. Cryst. 37, 335–338.
Berman, H. M., Battistuz, T., Bhat, T. N., Bluhm, W. F., Bourne, P. E., Burkhardt, K., Feng, Z., Gilliland, G. L., Iype, L., Jain, S., Fagan, P., Marvin, J., Padilla, D., Ravichandran, V., Schneider, B., Thanki, N., Weissig, H., Westbrook, J. D. & Zardecki, C. (2002). The Protein Data Bank. Acta Cryst. D58, 899–907.
Berman, H. M., Olson, W. K., Beveridge, D. L., Westbrook, J., Gelbin, A., Demeny, T., Hsieh, S.-H., Srinivasan, A. R. & Schneider, B. (1992). The Nucleic Acid Database: a comprehensive relational database of three-dimensional structures of nucleic acids. Biophys. J. 63, 751–759.
Bernstein, H. J. (1998). cif2cif. CIF copy program. http://www.iucr.org/iucr-top/cif/software/ciftbx/cif2cif.src/ .
Bernstein, H. J. & Hall, S. R. (1998). CIF applications. VII. CYCLOPS2: extending the validation of CIF data names. J. Appl. Cryst. 31, 278–281.
Bluhm, W. (2000). STAR (CIF) parser. http://pdb.sdsc.edu/STAR/index.html .
Brown, I. D., Zabobonin, A. & Holt, B. (2004). beCIF. Browser and editor for CIF. Private communication.
Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.
Edgington, P. R. (1997). HICCuP: High-Integrity CIF Checking using Python. Cambridge: Cambridge Crystallographic Data Centre.
Greer, D. S. (2000). Macromolecular structure RFP response. Revised submission.http://openmms.sdsc.edu/OpenMMS-1.5.1_Std/openmms/docs/specs/lifesci_00–11-01.pdf .
Greer, D. S., Westbrook, J. D. & Bourne, P. E. (2002). An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics, 18, 1280–1281.
Hall, S. R. (1993). CIF applications. III. CYCLOPS: for validating CIF data names. J. Appl. Cryst. 26, 480–481.
Hall, S. R., Allen, F. H. & Brown, I. D. (1991). The Crystallographic Information File (CIF): a new standard archive file for crystallography. Acta Cryst. A47, 655–685.
Hall, S. R. & Bernstein, H. J. (1996). CIF applications. V. CIFtbx2: extended tool box for manipulating CIFs. J. Appl. Cryst. 29, 598–603.
Hall, S. R. & Sievers, R. (1993). CIF applications. I. QUASAR: for extracting data from a CIF. J. Appl. Cryst. 26, 469–473.
Hester, J. R. (2006). A validating CIF parser: PyCIFRW. J. Appl. Cryst. 39, 621–625.
Hester, J. R. & Okamura, F. P. (1998). CIF applications. X. Automatic construction of CIF input functions: CifSieve. J. Appl. Cryst. 31, 965–968.
Knuth, D. E. (1986). The [\hbox{\TeX}]book. Computers and Typesetting, Vol. A. Reading, MA: Addison-Wesley.
McMahon, B. (1993). ciftex: translation utility from CIF to [\hbox{\TeX}]. ftp://ftp.iucr.org/pub/ciftex.tar.Z .
McMahon, B. (1998). vcif: a utility to validate the syntax of a Crystallographic Information File. http://www.iucr.org/iucr-top/cif/software/vcif/index.html .
OMG (2001). Life Sciences Research Domain Task Force. http://www.omg.org/lsr/ .
Ousterhout, J. K. (1994). Tcl and the Tk toolkit. Reading, MA: Addison-Wesley.
Painter, J. & Merritt, E. A. (2004). mmLib Python toolkit for manipulating annotated structural models of biological macromolecules. J. Appl. Cryst. 37, 174–178.
Patel, A. J. (2002). Yapps: Yet Another Python Parser System. http://theory.stanford.edu/~amitp/yapps/ .
Rossum, G. van (1991). Python programming language. http://www.python.org .
Spadaccini, N. & Hall, S. R. (1994). Star_Base: accessing STAR File data. J. Chem. Inf. Comput. Sci. 34, 509–516.
Stampf, D. R. (1994). ZINC: galvanizing CIF to work with UNIX. Brookhaven: Protein Data Bank.
Toby, B. H. (2003). CIF applications. XIII. CIFEDIT, a program for viewing and editing CIFs. J. Appl. Cryst. 36, 1288–1289.
Tosic, O. & Westbrook, J. D. (2000). CIFParse. A library of access tools for mmCIF. Reference guide. http://sw-tools.pdb.org/apps/CIFPARSE-OBJ/cifparse/index.html .
Wall, L., Schwartz, R. L., Christiansen, T. & Orwant, J. (2000). Programming Perl, 3rd ed. Sebastopol, CA, USA: O'Reilly & Associates, Inc.
Westbrook, J. D. & Bourne, P. E. (2000). STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics, 16, 159–168.
Westbrook, J. & Fitzgerald, P. (2003). The PDB format, mmCIF formats and other data formats. Structural bioinformatics, edited by P. E. Bourne & H. Weissig, pp. 161–179. Hoboken, NJ: John Wiley & Sons, Inc.
Westbrook, J. D., Hsieh, S.-H. & Fitzgerald, P. M. D. (1997). CIF applications. VI. CIFLIB: an application program interface to CIF dictionaries and data files. J. Appl. Cryst. 30, 79–83.
Westrip, S. P. (2004). printCIF for Word. http://www.iucr.org/iucr-top/cif/software/printCIFforWord/index.html .
Winn, M. (1998). cif.el: an Emacs mode for CIF. Daresbury Laboratory, Warrington, England.