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No. 17
Spring 2003

Front Page


Message from the PDB

PDB Deposition Statistics

PDB Annotation Manual Online in PDF and PostScript Formats

PDB Focus: ADIT Annotators

New Features Available for Beta Testing: Biological Unit, Curated (Beta) mmCIF Files, Redundancy Reduction Cluster Data

New Features on the Structure Explorer Pages of the PDB Web Site: Author and Ligand Searches, BioMagResBank Links

PDB Focus: Redundancy Reduction Capability

PDB Focus: Maintaining a Local PDB FTP Mirror Site

PDB Focus: Weekly Updates to the PDB

PDB Web Site Statistics

Structural Bioinformatics Book Includes Chapters on the PDB

PDB Paper Published in Nucleic Acids Research

New Distribution Procedure for Protein Data Bank CD-ROM Sets

PDB at the Biophysical Society Meeting

PDB Focus: David Goodsell and the Molecule of the Month

PDB Molecules of the Quarter: Serum Albumin, Potassium Channels, and lac Repressor

PDB Education Corner

Related Links: Education

PDB Job Listings

PDB Members & Statement of Support

Questions?
info@rcsb.org

© 2003 PDB

 

PDB Focus: Maintaining a Local PDB FTP Mirror Site

There are several freely available methods for establishing and maintaining a local copy of the PDB FTP Site. The methods described below have the added benefit of preserving the timestamps on files:

rsyncPDB.sh

The RCSB-created rsyncPDB.sh script is a template for using rsync to mirror the FTP archive from an anonymous rsync server. The script can be found at ftp://ftp.rcsb.org/pub/pdb/software/, and the comments in the script explain its usage. Before successfully running it, users will need to set three variables in rsyncPDB.sh to suit their local setup. This script is now used by the PDB to maintain its FTP mirrors.

mirror.pl

The non-RCSB mirror.pl script, which had been used to mirror the PDB FTP archive in the past, is available under the GNU public license from ftp://sunsite.org.uk/packages/mirror/. It is recommended to install the ftp.pl_wupatch security patch with the script, also available from this site.


The RCSB-created getPdbUpdate.pl script can also be useful for providers of new FTP mirror sites in obtaining the files from any one particular update. The script can be found at ftp://ftp.rcsb.org/pub/pdb/software/, and its usage is explained at ftp://ftp.rcsb.org/pub/pdb/software/getPdbUpdate.html. Be aware that only LWP::UserAgent, but not wget, preserves the original time stamps of the files.

PDB FTP mirroring procedures are further explained at http://www.rcsb.org/pdb/ftpproc.final.html, and the layout of the PDB FTP archive is accessible at http://www.rcsb.org/pdb/ftp_plan.html. For more information about mirroring the PDB FTP Site, please send e-mail to info@rcsb.org.