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
https://doi.org/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.Google Scholar
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.Google Scholar
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.Google Scholar
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.Google Scholar
Bernstein, H. J. (1998). cif2cif. CIF copy program. http://www.iucr.org/iucr-top/cif/software/ciftbx/cif2cif.src/ .Google Scholar
Bernstein, H. J. & Hall, S. R. (1998). CIF applications. VII. CYCLOPS2: extending the validation of CIF data names. J. Appl. Cryst. 31, 278–281.Google Scholar
Bluhm, W. (2000). STAR (CIF) parser. http://pdb.sdsc.edu/STAR/index.html .Google Scholar
Brown, I. D., Zabobonin, A. & Holt, B. (2004). beCIF. Browser and editor for CIF. Private communication.Google Scholar
Collaborative Computational Project, Number 4 (1994). The CCP4 suite: programs for protein crystallography. Acta Cryst. D50, 760–763.Google Scholar
Edgington, P. R. (1997). HICCuP: High-Integrity CIF Checking using Python. Cambridge: Cambridge Crystallographic Data Centre.Google Scholar
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 .Google Scholar
Greer, D. S., Westbrook, J. D. & Bourne, P. E. (2002). An ontology driven architecture for derived representations of macromolecular structure. Bioinformatics, 18, 1280–1281.Google Scholar
Hall, S. R. (1993). CIF applications. III. CYCLOPS: for validating CIF data names. J. Appl. Cryst. 26, 480–481.Google Scholar
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.Google Scholar
Hall, S. R. & Bernstein, H. J. (1996). CIF applications. V. CIFtbx2: extended tool box for manipulating CIFs. J. Appl. Cryst. 29, 598–603.Google Scholar
Hall, S. R. & Sievers, R. (1993). CIF applications. I. QUASAR: for extracting data from a CIF. J. Appl. Cryst. 26, 469–473.Google Scholar
Hester, J. R. (2006). A validating CIF parser: PyCIFRW. J. Appl. Cryst. 39, 621–625.Google Scholar
Hester, J. R. & Okamura, F. P. (1998). CIF applications. X. Automatic construction of CIF input functions: CifSieve. J. Appl. Cryst. 31, 965–968.Google Scholar
Knuth, D. E. (1986). The [\hbox{\TeX}]book. Computers and Typesetting, Vol. A. Reading, MA: Addison-Wesley.Google Scholar
McMahon, B. (1993). ciftex: translation utility from CIF to [\hbox{\TeX}]. ftp://ftp.iucr.org/pub/ciftex.tar.Z .Google Scholar
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 .Google Scholar
OMG (2001). Life Sciences Research Domain Task Force. http://www.omg.org/lsr/ .Google Scholar
Ousterhout, J. K. (1994). Tcl and the Tk toolkit. Reading, MA: Addison-Wesley.Google Scholar
Painter, J. & Merritt, E. A. (2004). mmLib Python toolkit for manipulating annotated structural models of biological macromolecules. J. Appl. Cryst. 37, 174–178.Google Scholar
Patel, A. J. (2002). Yapps: Yet Another Python Parser System. http://theory.stanford.edu/~amitp/yapps/ .Google Scholar
Rossum, G. van (1991). Python programming language. http://www.python.org .Google Scholar
Spadaccini, N. & Hall, S. R. (1994). Star_Base: accessing STAR File data. J. Chem. Inf. Comput. Sci. 34, 509–516.Google Scholar
Stampf, D. R. (1994). ZINC: galvanizing CIF to work with UNIX. Brookhaven: Protein Data Bank.Google Scholar
Toby, B. H. (2003). CIF applications. XIII. CIFEDIT, a program for viewing and editing CIFs. J. Appl. Cryst. 36, 1288–1289.Google Scholar
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 .Google Scholar
Wall, L., Schwartz, R. L., Christiansen, T. & Orwant, J. (2000). Programming Perl, 3rd ed. Sebastopol, CA, USA: O'Reilly & Associates, Inc.Google Scholar
Westbrook, J. D. & Bourne, P. E. (2000). STAR/mmCIF: an ontology for macromolecular structure. Bioinformatics, 16, 159–168.Google Scholar
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.Google Scholar
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.Google Scholar
Westrip, S. P. (2004). printCIF for Word. http://www.iucr.org/iucr-top/cif/software/printCIFforWord/index.html .Google Scholar
Winn, M. (1998). cif.el: an Emacs mode for CIF. Daresbury Laboratory, Warrington, England. Google Scholar