sf-convert: A Format
Conversion Tool for Structure Factor Files
The command-line program, sf-convert, can easily translate data
in various formats to the mmCIF format for use with ADIT validation
and deposition software. sf-convert can also translate structure
factors already released in the PDB from mmCIF to different formats.
This tool can input files from the following programs and formats:
mmCIF, CIF, MTZ, CNS, Xplor, HKL2000, Scalepack, Dtrek, TNT, SHELX,
SAINT, EPMR, XSCALE, XPREP, XTALVIEW, X-GEN, XENGEN, MULTAN, MAIN,
and OTHER (an ASCII file with H, K, L, F, and SigmaF separated by
sf-convert can then output the data formatted as mmCIF, MTZ, CNS,
TNT, SHELX, EPMR, XTALVIEW, HKL2000, Dtrek, XSCALE, MULTAN, MAIN,
sf-convert is available for download from sw-tools.pdb.org.
Deposit EM Maps at the MSD-EBI or RCSB PDB
microscopy map data can now be deposited to the Electron Microscopy
Data Bank (EMDB) using the improved web-based tool EmDep2. EmDep2
is available from the existing deposition site at the MSD-EBI in
Europe and also from a new deposition site at the RCSB PDB in the
The EMDB contains experimentally determined 3D maps and associated
experimental data and files.
This improvement to EMDB services is the first product of a collaboration
between the European Network of Excellence 3D-EM (www.3dem-noe.org)
and the recently NIH-funded Partnership for a Unified Data Resource
for CryoEM (emdatabank.org)
This partnership is comprised of the European Bioinformatics Institute,
the Research Collaboratory for Structural Bioinformatics at Rutgers,
and the National Center for Macromolecular Imaging at Baylor College
EmDep2 (EBI): www.ebi.ac.uk/msd-srv/emdep
EmDep2 (RCSB PDB): emdb.rutgers.edu/emde.
A. Fokine, A. Battisti, V. Bowman,
A. Efimov, L. Kurochkina, P. Chipman, V. Mesyanzhinov, M. Rossmann
Cryo-EM Study of the Pseudomonas Bacteriophage phiKZ Structure
(2007) 15: 1099-1104
In the first quarter of 2008, 1626 experimentally-determined
structures were deposited to the PDB archive.
The entries were processed by wwPDB teams at the RCSB PDB, MSD-EBI,
and PDBj. Of the structures deposited in the first quarter of 2008,
75% were deposited with a release status of "hold until publication";
22.5% were released as soon as annotation of the entry was complete;
and 2.5% were held until a particular date.
90% of these entries were determined by X-ray crystallographic
methods; 9% were determined by NMR methods. 97% of these depositions
were deposited with experimental data. As of February 1, 2008, the
deposition of experimental data is required.
During the same period of time, 1915 structures were released into
Processing Versioning Procedures
Data in the PDB archive currently follow
either PDB File Format Version 3.0 or 3.1. This is indicated in
REMARK 4 of the file.
Version 3.0 is the format used for files released
as a result of the Remediation Project.
Since August 1, 2007, all files processed and
released into the archive have followed Version 3.1. When modifications
have been made to files released prior to that date, they have been
then re-released in Version 3.1.
Version 3.1 differs from Version 3.0 in descriptions
of the biological unit (REMARK 300/350), geometry (REMARK 500),
atom/residues modeled as zero occupancy (REMARK 475/480), non-polymer
residues with missing atoms (REMARK 610), and metal coordination
(REMARK 620). Documentation describing the differences between these
versions is available at www.wwpdb.org/docs.html.
Since the beginning of March 2008, the REVDAT
record indicates when a Version 3.0 file is re-released as Version
3.1 with the name "VERSN." For example, if the journal record has
been updated in an entry that previously followed Version 3.0, the
REVDAT would appear as:
1 04-MAR-08 1ABC 1 JRNL VERSN
1 13-FEB-07 1ABC 0
There is no change to how depositors submit
their files. Any required changes in nomenclature can be made automatically
by the wwPDB during the annotation process.
Documentation about file formats and the Remediation
Project is available at www.wwpdb.org.