PDB Focus: Beta FTP Site Organized by Experimental Type

The RCSB has introduced a new ftp site designed to address the increasing number and diversity of structure entries. Entries within ftp://ftpbeta.rcsb.org are organized by the method of structure determination. This new ftp structure distinguishes entries obtained from X-ray and neutron diffraction, NMR, electron microscopy, or theoretical modeling techniques.

Within each structure determination category, there are directories containing files for entries in mmCIF, PDB, and XML formats; biological unit files; and the structure factor or restraint files. Individual entries are stored in a collection of 2-letter code subdirectories corresponding to the middle characters of the 4-letter PDB identifier.

All entries in the new ftp site are compressed using the GNU gzip utility. For example, the PDB format file for entry 4HHB is found at ftp://ftpbeta.rcsb.org/pub/data_by_method/
x-ray_neutron_methods/entries/pdb/hh/pdb4hhb.ent.gz.

This beta ftp site is updated weekly in conjunction with the current ftp site, ftp://ftp.rcsb.org. Both ftp sites will be maintained through December 2005. After this time, only the new organization will be supported.

For comments about the beta FTP send mail to betaftp@rcsb.rutgers.edu.

WEBSITE STATISTICS

The access statistics are given or the primary RCSB PDB website at www.pdb.org.

Data Distribution on DVD

As of 2005, the PDB archives will be made available as an annual DVD product. The CD-ROM product has been discontinued.

The PDB has historically distributed coordinate data through the mail; starting in 1990, the data were produced on CD-ROM. In addition to the rapid increase in the number and size of structures in the archives, the number of formats to distribute has also increased (to PDB, mmCIF, and PDBML/XML). Currently, it would take over 50 disks to distribute the archives on CD-ROM.

To minimize the difficulty of producing (and keeping up with a large number of CDs), the RCSB PDB began distributing an incremental set of data each quarter in April 2003.

Starting in January 2005, ftp://snapshots.rcsb.org/ was created to hold time-stamped yearly snapshots of the PDB archives. This was done as part of a wwPDB initiative (wwpdb.org). The first snapshot directory contains the exact and complete contents of the FTP archives as it appeared on January 6, 2005. These data, along with data in XML/PDBML format, were also made available as an 8 DVD release.

To order a DVD set, please email your postal address to cddvd@rcsb.rutgers.edu. New orders will be filled in the order that they are received until supplies are exhausted. Please allow several weeks for delivery.