RCSB PDB Newsletter #20: Downloadable PDB_EXTRACT Makes Deposition Easier

No. 20
Winter 2004


Message from the RCSB PDB

Announcing the Worldwide Protein Data Bank

Downloadable PDB_EXTRACT Makes Deposition Easier

Biological Unit Tutorial Now Available from the RCSB PDB

Ligand Depot--a Small Molecule Information Resource

PDB Focus: Deposition and Release Policies

PDB Deposition Statistics

Lucene Keyword Search Released on the RCSB PDB Web Site

PDB Focus: Redundancy Reduction Cluster Data Available on the PDB FTP Site

PDB Focus: Searching for Experimental Data Files

Updates of mmCIF Files on the RCSB PDB FTP Site

RCSB PDB Web Site Statistics

NIGMS News: PSI-2 and Structural Biology Roadmap RFA

RCSB PDB Article Published in Nucleic Acids Research

New Update Release of CD-ROM Sets

PDB Molecules of the Quarter: Trypsin, Simian Virus 40, and Catabolite Activator Protein

PDB Community Focus: Edward N. Baker

PDB Education Corner by Katherine Kantardjieff

Related Links: FTP Resources

RCSB PDB Job Listings

RCSB PDB Members & Statement of Support

Questions? info@rcsb.org

© 2004 RCSB PDB


Downloadable PDB_EXTRACT Makes Deposition Easier

The software program PDB_EXTRACT was developed to assist depositors in the automatic preparation of crystallographic depositions. This software tool extracts information for deposition from the output files produced by many applications used for structure determination. Current versions of the following programs are supported: HKL 2000, SCALEPACK, d*TREK, SOLVE, MLPHARE, SHARP/autoSHARP, SHELXD/SHELXE/SHELXL, PHASES, SnB, BnP, DM, Solomon, RESOLVE, CNS, REFMAC, RESTRAIN, TNT, and WARP. PDB_EXTRACT will also be part of the CCP4 Program Suite (version 5).

Files produced by PDB_EXTRACT can be edited on a local Linux workstation using the downloadable version of ADIT, which has been extended to provide access to the large amount of data collected by the PDB_EXTRACT program.

PDB_EXTRACT can be downloaded in source and binary versions for Linux, SGI, SUN, OSF and Mac OSX from deposit.pdb.org/software. Source and Linux binary versions of ADIT are also available.

Questions and comments may be sent to help@rcsb.rutgers.edu.