Published quarterly by the Research Collaboratory
for Structural Bioinformatics Protein Data Bank

Winter 2008
Number 36

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Data Deposition
• 2007 Deposition Statistics
• ADIT Beta Available for Testing
• New Release of pdb_extract Deposition Tool
• Announcement: Experimental Data Will Be Required for Depositions Beginning February 1, 2008
• Structure Deposition Checklist

Data Query, Reporting and Access
• Website Statistics
• Automated Downloads of PDB Data
• RCSB PDB Focus: Sorting Search Results
• Positions Available at the RCSB PDB

Outreach and Education
• Web Survey: RCSB PDB Educational Resources
• Poster Prize Awarded at AsCA
• Flyers Available in Print and Online
• 2008 Calendar Now Available
• RCSB PDB Paper Cited More Than 5,000 Times

Education Corner
Fruit-flavored Folding by Teresa MacDonald, Director of Education at The University of Kansas Natural History Museum

PDB Community Focus

Protein Modeling at the New Jersey Science Olympiad Regionals



Website Statistics
The RCSB PDB website at began to utilize the data from the wwPDB remediation project starting August 1, 2007. Access statistics for this website are given below.


Unique Visitors
Aug 2007
380.69 GB
Sep 2007
482.76 GB
Oct 2007
608.34 GB
Nov 2007
662.43 GB
Dec 2007
408.06 GB


Automated Downloads of PDB Data from

As previously announced, the PDB archive has been moved to

Updated weekly, this location maintains the files from the wwPDB Remediation Project and all newly released files. The archive currently contains approximately 350,000 files, including coordinate data in PDB, mmCIF, and PDBML/XML formats, and experimental data. Since the entire archive requires more than 70 GB of storage, fresh downloads require a substantial amount of time. In December 2007, more than 27 million files were downloaded from

During the same period, approximately 2.4 million files were downloaded from the snapshot of unremediated data at Users should be aware that this site is no longer updated, and are strongly encouraged to update any automatic scripts or bookmarks to
Data files from the archive can be accessed online in a variety of ways, including:

The online Structure Download tool is accessible from the Download Files
section of the left hand menu. PDB IDs can be entered in the box provided.

At, users will find download information for downloading:

  • A single file via ftp
  • The entire archive via rsync
  • All files in a given format (PDB, CIF, XML) via rsync
  • The entire archive via ftp
  • All files in a given format (PDB, CIF, XML) via ftp using tar balls

RCSB PDB Focus: Sorting Search Results

Following a search that produces multiple entries, the results set can be sorted by choosing 'Sort Results' from the menu on the left hand side of the page.

For most searches, the sorting options include: PDB ID, Release Date, Residue Count, Resolution and Rank (useful with keyword searches).

An Advanced Search by sequence (Advanced Search >> Sequence Features >> Sequence (Blast/Fasta)) allows the user to sort results by PDB ID, formula weight and E value.


Structures matching your search constraints can be sorted according to ID, release date,
residue count, resolution, and the rank of how closely they match the query (shown in green)

Positions Available at the RCSB PDB

The RCSB PDB has the following positions available:

  • Senior Scientist/Scientific Software Developer (UCSD)
  • Lead Web Architect (UCSD)
  • Biochemical Information & Annotation Specialist (Rutgers)
For more information, select the “Job Listings” link at


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