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pdb_extract - Workstation Version

The pdb_extract Program Suite contains tools and examples for extracting mmCIF data from structure determination applications.

  • Reduce the human effort required to assemble complete and validated protein structure entries ready for PDB deposition via ADIT.
  • Faster preparation of your mmCIF file for deposition.
  • Great for multiple structural depositions. The data template file can be re-used for each structure without re-entering the same information.

A pdb_extract manual is accessible via online and downloadable PDF detailing procedures concerning program installation and use.

Program Access

The binary (recommended) and source versions of pdb_extract are available for download. The binary distributions are available for Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris. The source is available under an Open Source license.

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
System Requirements
  • Platforms: Intel-Linux, SGI-IRIX, DEC-Alpha, and Sun-Solaris
  • Disk space greater than 30 Mbytes for binary distribution
  • Disk space greater than 140 Mbytes for source distribution
  • C/C++ compilers

 

 

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