THE NUCLEIC ACID DATABASE NEWSLETTER, November 2000, Volume 4, Number 2
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ANNOUNCEMENT: NDB to release files from data uniformity processing


mmCIF Dictionary updated
Music Atlas highlighted in Science

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ANNOUNCEMENT: NDB to release files from data uniformity processing

On November 27, 2000, the NDB will re-release approximately 1000 files
resulting from data uniformity processing.  These NDB files will be released
in both PDB and mmCIF formats.

All of the PDB formatted files provided in this release are in the format
currently used by the PDB [1].  Any differences in content in these PDB files
are small as compared to previous version of these files provided by the NDB.
Some records, particularly those dealing with sequence database
correspondences, have been reviewed and updated.

The PDB format files that have been modified as a part of the data uniformity
processing will have a REVDAT modification type ("modType") of 5:

REVDAT   2   27-NOV-00 1ABC    5 

These new PDB format files be available from the NDB ftp server in the
directory ftp://ndbserver.rutgers.edu/pub/coordinates/na-chiral-correct/

The mmCIF files follow the latest version of the mmCIF dictionary supplemented
by an exchange dictionary developed by the PDB and the European Bioinformatics
Institute.  This exchange dictionary can be obtained from
http://mmcif.rcsb.org/.  These mmCIF files are complete, rather
than the abbreviated mmCIF format formerly distributed by the NDB.

The new mmCIF format files be available from the NDB ftp server in the
directory ftp://ndbserver.rutgers.edu/pub/coordinates/na-mmcif/.  These files
will also be available shortly from the PDB beta ftp site,
ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/.

These files will also be available at the NDB mirrors.

This update will increase the size of the ftp site by approximately 230
MegaBytes.

[1]  Protein Data Bank Contents Guide: Atomic Coordinate Entry Format 
     Description, Version 2.2, October, 1996.  
     http://www.rcsb.org/pdb/docs/format/pdbguide2.2/guide2.2_frame.html

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mmCIF Dictionary

Version 2.0.03 of the Macromolecular Crystallographic Information File
Dictionary is now available at the mmCIF site at 

http://mmcif.rcsb.org/dictionaries/mmcif_std.dic/Index/index.html/

A document listing the Recommended PDB -> mmCIF Data Item Correspondences is
also available from the mmCIF site at http://mmcif.rcsb.org/index.html.


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Music Atlas highlighted in Science

The NDB Musical Atlas was highlighted in the NetWatch section of Science
(Volume 290, Number 5494).  The Atlas uses different musical algorithms to
provide a unique look into the structure of DNA.

NDB Music Atlas:  
http://ndbserver.rutgers.edu/atlas/music/index.html


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The Nucleic Acid Database Project Members: Helen M. Berman, Zukang Feng, Lisa
Iype, Xiang-Jun Lu, Wilma K. Olson, Bohdan Schneider, John Westbrook and
Christine Zardecki

Comments and questions should be sent to ndbadmin@ndbserver.rutgers.edu

The Nucleic Acid Database Project is funded by the 
National Science Foundation and the Department of Energy

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