RCSB PDB Newsletter #20: PDB Focus: Searching for Experimental Data Files

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


PDB Focus: Searching for Experimental Data Files

The PDB offers several ways to locate experimental data files for structure entries. The SearchFields interface offers an option to narrow a search to only include entries that have experimental data (X-ray structure factors or NMR restraints) available. This option can be activated by selecting "Experimental Data Availability" from the custom options at the bottom of the SearchFields page. To further narrow the search to only structure factors or only constraint data, select the preferred experimental method from the pull down menu in the "Exp. Technique" field. Information about this and other options available on the SearchFields interface can be found on the SearchFields help page.

Experimental data files can be downloaded from the Structure Explorer page, if the experimental data file is available for that structure. Click on the "Structure Factors" or "NMR Restraints" link on the left side of the page to access the experimental data file.

Experimental data files are also available for downloading from the RCSB PDB FTP site. Directories for either X-ray structure factors or NMR restraints can be found at ftp://ftp.rcsb.org/pub/pdb/data/structures/all/, or subdivided by the second and third character of their PDB IDs at ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/. Experimental data files for structures that have been removed from the archive can be found at ftp://ftp.rcsb.org/pub/pdb/data/structures/obsolete/.

A search for PDB entries that include experimental data can be performed from the SearchFields interface by selecting the "Yes" radio button in the Exp. Data Available field, as indicated in the screenshot above.