PDB_EXTRACT

Description

The PDB_EXTRACT program suite contains tools and examples for extracting mmCIF data from structure determination applications.

Distribution

• current version (RCSB web site)

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 However, they may be out of date and lack the full functionality of the latest version.

• stable source for Unix: Unix gzipped tar file pdb-extract-v3.004-prod-src.tar.gz
• individual source files
• binary distribution for Linux (gzipped tar archive)
• binary distribution for Silicon Graphics Irix (gzipped tar archive)
• binary distribution for Sun Solaris (gzipped tar archive)
• binary distribution for OSF (gzipped tar archive)
• binary distribution for Mac OS X (gzipped tar archive)

Status

PDB_EXTRACT is under constant development as a tool to allow the creation of mmCIF files from a variety of current macromolecular structure determination packages. The version distributed here is version 3.004 of September 2007. Users are recommended to obtain the latest release from the Rutgers site of the Research Collaboratory for Structural Bioinformatics (RCSB) if at all possible. Comments should be directed to jwest@rcsb.rutgers.edu.

An online version of PDB_EXTRACT can be accessed at http://pdb-extract.rcsb.org.

PDB_EXTRACT has been integrated into CCP4 and the CCP4i interface (Version 5.0 and above). Users can run PDB_EXTRACT under the CCP4 environment.

Supported Applications

A comprehensive list of supported applications detailing software category, version, and references is available.

• X-Ray Software Applications: AMORE (CCP4), ARP/wARP, BnP , CNS/CNX/XPLOR , D*trek , DM (CCP4), EPMR, HKL/SCALEPACK , MLPHARE (CCP4), MOLREP (CCP4), MOSFLM , PHASER, PHASES, PHENIX , REFMAC5 (CCP4) , RESOLVE, RESTRAIN (CCP4) , SAINT , SCALA (CCP4) , SHARP/autoSHARP , SHELXD/SHELXS , SHELXE , SHELXL, SnB , SOLOMON (CCP4), SOLVE, TNT , XSCALE
• NMR Software Applications: CNS/CNX/XPLOR, CYANA

Language and platform

The software is written in C++ and should run on versions of Unix with suitable C++ compilers. Binary distributions are provided for Linux, SGI, Sun, OSF and Mac OS X platforms. The binary distributions also include the structure checking module PROCHECK.

Documentation

• Installation from source distribution: For Unix-type installations, copy the gzipped tar file pdb-extract-v3.004-prod-src.tar.gz into an empty directory; gunzip and extract files using the Unix tar utility. Set appropriate environment variables (see detailed installation notes); build the application using the make utility; create binary data files. E.g.

   cp pdb-extract-v3.004-prod-src.tar.gz /p/q/r; cd /p/q/r
   cat pdb-extract-v3.004-prod-src.tar.gz | gunzip | tar xvf -
   cd /p/q/r/pdb-extract-v3.004-prod-src
   RCSBROOT=/p/q/r/pdb-extract-v3.004-prod-src; export RCSBROOT
   PATH="$RCSBROOT/bin:"$PATH; export PATH
   make
   make binary 

  If gzip or tar are unavailable, individual source files may be saved to the build directory.
  For more details see the Installation Notes
• Installation from binary distribution: For Unix-type installations, copy the relevant gzipped tar file pdb-extract-v3.004-prod-bin-xxx.tar.gz into an empty directory; gunzip and extract files using the Unix tar utility. Set appropriate environment variables (see detailed installation notes); create binary data files. E.g.

   cp pdb-extract-v3.004-prod-bin-xxx.tar.gz /p/q/r; cd /p/q/r
   cat pdb-extract-v3.004-prod-bin-xxx.tar.gz | gunzip | tar xvf -
   cd /p/q/r/pdb-extract-v3.004-prod-bin-xxx
   RCSBROOT=/p/q/r/pdb-extract-v3.004-prod-bin-xxx; export RCSBROOT
   PATH="$RCSBROOT/bin:"$PATH; export PATH
   cd etc
   ./binary.sh 

  For more details see the Installation Notes
• Documentation for the stand-alone PDB_EXTRACT ( HTML | PDF format )

Terms and conditions of use

Copyright in the software © Rutgers - The State University of New Jersey
Authors: John Westbrook and colleagues

The software is distributed here under licence from the Protein Data Bank/RCSB. Use of the software is governed by the PDB software licence. Queries concerning any other use should be directed to sw-help@rcsb.rutgers.edu.