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
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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.

pdb2cif

Description

pdb2cif (Bernstein et al., 1998) is a script to filter a PDB entry and produce an mmCIF.

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 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 However, they may be out of date and lack the full functionality of the latest version.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 2.4.2 of 6 October 2004.

Language and platform

The scripts are written in perl, awk or old-awk and should run on any common operating system that supports perl or has suitable versions of awk. On some systems, one may need to use gawk instead of awk. pdb2cif.awk uses features which are not found in the original Aho, Kernighan & Weinberger Awk - a pattern scanning and processing language, but which have since been added on most systems: functions and the call to 'system'.

Documentation

  • Installation: Copy the selected archive (pdb2cif.cshar.Z or pdb2cif.shar.Z - only one is required) into an empty directory. In this directory, uncompress the selected archive and execute it with the C or Bourne shell as appropriate. 
    cp pdb2cif.shar.Z /x/y/base
    cd /x/y/base
    uncompress pdb2cif.shar.Z
    sh pdb2cif.shar
    Select the script suitable for running under the interpreter of choice and make it executable. On most Unix systems, this can be done by executing one of the following sets of commands, depending on whether you want the perl, awk, or old-awk version to be pdb2cif: 
    chmod 755 pdb2cif.pl
    ln -s pdb2cif.pl pdb2cif

    chmod 755 pdb2cif.oawk
    ln -s pdb2cif.oawk pdb2cif

    chmod 755 pdb2cif.awk
    ln -s pdb2cif.awk pdb2cif
  • General information: README file (HTML format)

Terms and conditions of use

Copyright in the software © the authors.
Authors: P. E. Bourne, 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, 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.