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.
|
|
|
