During this past quarter, several new developments that were previously in beta test have
been incorporated into the primary PDB web site, its mirrors, and on the PDB FTP site:
Remediated mmCIF Files
The primary PDB Web site and its mirrors now offer the remediated mmCIF files, previously
referred to as the "beta" mmCIF files. These files have replaced the set of automatically
translated mmCIF files that were created with pdb2cif.pl. The remediated files can be
accessed from the Download/Display File section of the Structure Explorer page for any
entry, or for a set of query results.
The remediated mmCIF files are also available from the PDB FTP site at
ftp://ftp.rcsb.org/pub/pdb/data/structures/all/mmCIF/. The translated files have been
removed from the FTP site, and will be made available upon individual request.
For every experimentally-solved structure, both current and obsolete, there is now a
remediated mmCIF file in the corresponding directory of the FTP archive in Unix compressed
(.Z) format. mmCIF files are not provided for theoretical models. However, the translation
software (pdb2cif.pl) is provided at www.bernstein-plus-sons.com/software/pdb2cif
for users who wish to generate the translated mmCIF files.
Biological Unit Images and Coordinate Files
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. 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.
Biological unit coordinate files are also available from the FTP archive at
ftp://ftp.rcsb.org/pub/pdb/data/biounit. These files are accessible in gzipped (.gz) format. Links to a variety of free uncompression tools can be found at www.rcsb.org/pdb/help-general.html#format_structure_compressed.
Enzyme Names and EC Number Query
The Summary Information section of the Structure Explorer page for enzymes in the PDB now
displays the enzyme name for entries with complete EC numbers. This section also supports
queries for all other PDB entries with the same EC number by clicking on the number shown
for that entry.
Questions about these new features may be sent to firstname.lastname@example.org.
PDB ID: 1nkp
Nair, S. K., Burley, S. K. (2003): X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell 112, pp. 193-205.
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