International Tables for Crystallography

Volume G: Definition and exchange of crystallographic data

First online edition (2006)

Edited by S. R. Hall and B. McMahon
[International Tables Vol. G] contents
indexes
sample pages
purchase
CIF dictionaries

Describes CIF, the data exchange standard of crystallography. Provides: information for scientists who wish to record or use the results of a single-crystal or powder diffraction experiment; the data ontology necessary for designing interoperable computer applications; accompanying software including machine-readable CIF dictionaries, libraries and utility programs.

An essential guide and reference to CIF for programmers, data managers handling crystal-structure information and practising crystallographers.

cif2pdb

Description

cif2pdb (Bernstein & Bernstein, 1996) is a program for converting an mmCIF data set to a partial pseudo-PDB entry with HEADER, TITLE, COMPND, SOURCE, KEYWRD, AUTHOR, JRNL, REMARK 1, REMARK 960, SEQRES, CRYST1, ORIGX, SCALE, ATOM, ANISOU, SIGUIJ (starting from U's or B's), HETATM, MASTER and END records. Fractional or orthogonal coordinates may be provided in the mmCIF data set. If an mmCIF dictionary or other dictionary with the necessary aliases between mmCIF and the core is provided, the program can convert core CIF data sets. This is sufficient to drive RASMOL.

Distribution

If you wish to install and use this software you should download the most up-to-date version from the above Web site. The links below are to copies which are suitable for browsing or for use if the primary Web site is not available. However, they may be out of date and lack the full functionality of the latest version.

Status

This is Version 1.0.2 of 3 July 2002.

Language and platform

cif2pdb is written in Fortran as a CIFtbx application.

Documentation

  • Installation: Copy the selected archive (cif2pdb.cshar.Z or cif2pdb.shar.Z - only one is required) into a directory parallel to the installation directory for ciftbx. In this directory, uncompress the selected archive and execute it with the C or Bourne shell as appropriate. 

            top level directory (= x/y/base)
            --------------------------------
                           |
           ----------------------------------
           |                                |
        ciftbx                        cif2pdb_1.0.2
        ------                        -------------
           |
      ciftbx.src
      ----------

    cd /x/y/base
    mkdir cif2pdb_1.0.2
    cd cif2pdb_1.0.2
    cp .../cif2pdb.shar.Z /x/y/base/cif2pdb_1.0.2
    uncompress cif2pdb.shar.Z
    sh cif2pdb.shar
  • In order to compile you will need a copy of ciftbx. In order to recreate the test output you will need a copy of the mmCIF dictionary. Compilation is controlled by Makefile, which may need changes for the target system. Changes can be made by editing Makefile, if necessary, but in most cases it is easier to edit the m4 document, Makefile.m4, and then 
     make Makefile_local
    which will replace the current Makefile. Then cif2pdb can be compiled and tested by 
     make cif2pdb
     make tests
  • General information: README file (HTML format)

Terms and conditions of use

Copyright in the software © the authors.
Authors: H. J. Bernstein & F. C. Bernstein

The software is distributed here under an open-source license. Queries concerning any use not covered under this license should be directed to yaya@bernstein-plus-sons.com.

References

Bernstein, F. C. & Bernstein, H. J. (1996). Translating mmCIF data into PDB entries. Acta Cryst. A52 (Suppl.), C-576. [details]

Hall, S. R. & Bernstein, H. J. (1996). CIF applications. V. CIFtbx2: extended tool box for manipulating CIFs. J. Appl. Cryst. 29, 598-603. [details]