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No. 17
Spring 2003

Front Page


Message from the PDB

PDB Deposition Statistics

PDB Annotation Manual Online in PDF and PostScript Formats

PDB Focus: ADIT Annotators

New Features Available for Beta Testing: Biological Unit, Curated (Beta) mmCIF Files, Redundancy Reduction Cluster Data

New Features on the Structure Explorer Pages of the PDB Web Site: Author and Ligand Searches, BioMagResBank Links

PDB Focus: Redundancy Reduction Capability

PDB Focus: Maintaining a Local PDB FTP Mirror Site

PDB Focus: Weekly Updates to the PDB

PDB Web Site Statistics

Structural Bioinformatics Book Includes Chapters on the PDB

PDB Paper Published in Nucleic Acids Research

New Distribution Procedure for Protein Data Bank CD-ROM Sets

PDB at the Biophysical Society Meeting

PDB Focus: David Goodsell and the Molecule of the Month

PDB Molecules of the Quarter: Serum Albumin, Potassium Channels, and lac Repressor

PDB Education Corner

Related Links: Education

PDB Job Listings

PDB Members & Statement of Support

Questions?
info@rcsb.org

© 2003 PDB

 

New Features Available for Beta Testing: Biological Unit, Curated (Beta) mmCIF Files, Redundancy Reduction Cluster Data

During the past quarter, several new features have been released for beta testing:

Biological Unit -- Images and Coordinate Files

The biological unit images and corresponding coordinate files for applicable structures are now accessible from the Structure Explorer pages on the PDB Beta Web Site at http://beta.rcsb.org/pdb/.

The View Structure section of the Structure Explorer now offers still ribbon images of the assumed biological unit(s) for structures, where relevant, in addition to static images of the asymmetric unit. The interactive molecular viewers available from this page continue to provide a variety of ways to visualize the asymmetric unit. Links to the coordinate files that are used to generate the biological unit images are also accessible here, as well as from the Download/Display File section of the Structure Explorer.

Curated (Beta) mmCIF Files

The Download/Display File section of the Structure Explorer pages on the Beta Web Site now provides links to view or download the curated mmCIF files. These files include remediated data from the Data Uniformity Project (http://www.rcsb.org/pdb/uniformity/). The files follow the latest version of the mmCIF dictionary supplemented by an exchange dictionary developed by the RCSB and the MSD-EBI. This exchange dictionary can be obtained from http://deposit.pdb.org/mmcif/.

The curated mmCIF files for a set of query results can be downloaded by selecting the Download Structures or Sequences option from the pull down menu at the top of the Query Result Browser page.

Curated mmCIF files for all PDB structures are available in gzip (.gz) format at ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF.gz/. UNIX-compressed versions of these files (.Z) remain available at ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/.

Redundancy Reduction Cluster Data

The results of the weekly clustering of protein chains in the PDB are now available for beta testing at ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/. These clusters are used in the "remove sequence homologs" feature on the PDB web sites. Files that list the clusters and their rankings at 50%, 70% and 90% sequence identity are available. Smaller rank numbers indicate higher (better) ranking. Chains with rank number 1 are ranked as the best representative of their cluster.

The contents of these files and the details of the clustering and ranking are further described at ftp://ftp.rcsb.org/pub/pdb/derived_data/NR/README and http://www.rcsb.org/pdb/redundancy.html.

Comments on these new features are appreciated and may be sent to notify@rcsb.org.

The biological unit of Tn5 transposase complexed with Me DNA

PDB ID: 1mm8
Steiniger-White, M., Bhasin, A., Lovell, S., Rayment, I., Reznikoff, W. S. (2002): Evidence for "Unseen" Transposase--DNA Contacts. J. Mol. Biol. 322, p. 971.