PDB Focus: pdb_extract Makes Deposition Easier

pdb_extract helps depositors automatically prepare crystal structure depositions. This software tool extracts information about data collection, phasing, density modification, and the final structure refinement from the output files produced by many applications used for structure determination. The collected information is organized into an mmCIF file that is ready for deposition. Fewer data items have to be manually entered -- saving time and minimizing errors.

pdb_extract can be downloaded in source and binary versions for Linux, SGI, SUN, OSF and Mac OSX from Source and Linux binary versions of ADIT are also available.

pdb_extract is also part of the CCP4i interface.


In the first half of 2005, 3168 experimentally-determined structures were deposited to the PDB archive.

The entries were processed by wwPDB team members at RCSB-Rutgers, MSD-EBI, and PDBj. Of the structures deposited, 67% were deposited with a release status of HPUB; 17% with HOLD; and 16% with REL.

78% of these entries were determined by X-ray crystallography; 19% were determined by NMR. 80% were deposited with experimental data. 52% released the sequence in advance of the structure's release.