RCSB PDB BETA SITE FEATURES
2004, the RCSB PDB released a reengineered beta site
(pdbbeta.rcsb.org) for public testing. Some of the features of this site are described below.
Comments and suggestions about the beta site are welcomed at firstname.lastname@example.org.
- Query-by-Example in Structure Explorer Pages
The Structure Explorer page for any PDB entry can perform several "query-by-example" searches. Using the information available in a particular entry, structures containing the same data can be quickly found by clicking on that data item.
For example, all other entries by a specific primary citation author can be found by clicking on the author's name. A search of the database for all structures in which the selected author appears in the citation will be presented in a Query Results Browser.
Authors, Primary Citation Authors, Chemical Components, and GO, CATH,
and SCOP classifications can all be used in "query-by-example"
Query-by-Example: Selecting the author name "Wüthrich, K."
Returns all PDB entries with that author in the primary citation.
- Detailed Help System
The beta site uses Macromedia® RoboHelp® software
to offer detailed guidance for navigating the site and
understanding the information available from the RCSB
PDB. The integrated system organizes all the help pages on
the site and offers a table of contents, index, and glossary
on every page. These tools help users to access the rich
content offered by the help pages.
The help system launches into a separate browser window to
allow users to access the help information and the beta site
at the same time. Once users are in the RoboHelp system,
they can access help on specific topics by browsing through
the table of contents in the left hand menu. These topics
include Getting Started, Deposit Data, Validate Data,
Download Files, FTP Server, Search/Browse the Database,
Query Results Browser, and Viewing Molecules.
The Help link located at the top of the home page launches
the system. Links to specific help features and topics (such
as "How to Validate Data", "How to
Search", and "Molecular Viewer Help") are
located in the left hand navigation bars, menus and pages
throughout the website. An introduction to using RoboHelp on
the beta site is available.
The Glossary offered by the help system provides definitions
for terms related to structural biology, and is an excellent
source of information.
The beta site help system
- New Customizable Tabular and Structure Reports
Customizable reports are now available as a new feature on the
beta site. Users can select specific data items to display for
individual structures or for a group of structures. These
reports can be saved in a CSV format that can be opened in
spreadsheet application programs.
Individual customizable reports can consolidate information
from the four major areas of the "Summarize" pulldown menu
found on the 'Structure Explorer' page (Biology and Chemistry,
Materials and Methods, Sequence Details and Structural
Features). The report also can display information specific
for the type of the experimental method (X-Ray and NMR). In
addition, the report can also provide ligand details, SCOP and
CATH classifications, and the primary citation. An option to
generate a custom structure report can be found in the
pulldown menu on the 'Structure Explorer' page for a single
structure. These reports include images of the asymmetric and
biological units. A PDF can be viewed and saved by clicking on
the 'Print Page' link in the navigation bar at the top of the
Reports for a set of structures can include information from a
variety of areas, including Sequence, Ligands, Biological
Details, and Experimental Details. After selecting the set of
structures, these reports can be generated by using the
"Customize Report" option from the "Report" pulldown menu on
the 'Query Results Browser' page. The report generated can be
sorted in ascending/descending order of any column by clicking
on the column headers.
TIME-STAMPED COPIES OF PDB ARCHIVE AVAILABLE VIA FTP
tarting with January
2005, time-stamped yearly snapshots of the PDB Archive will be
available from ftp://snapshots.rcsb.org/. It is hoped that
these snapshots will provide readily identifiable data sets for
research on the PDB archive.
Currently, the directory 20050106 is available. This directory
contains the exact and complete contents of the FTP archive as it
appeared on January 6, 2005. This includes the 29040
experimentally-determined coordinate files that were current
(i.e., not obsolete) in PDB and mmCIF formats. Data in XML
(PDBML) format are not included in this first snapshot, but will
be made available on DVD in the near future. Subsequent snapshots
on this FTP server will include data in PDB, mmCIF, and PDBML
This snapshot follows the historical directory structure -- coordinate files are contained in
subdirectories named after the two middle characters of the PDB
ID, for example, 100d is found in the directory '00'.
The date and time stamp of each file indicates the last time the
file was modified. Entries in the PDB archive have been processed
by the three members of the wwPDB (RCSB, MSD-EBI, and PDBj).
he PDB is
available from several Web and FTP sites located around the
world. Users are also invited to preview new features at the RCSB
PDB beta test site, accessible at pdbbeta.rcsb.org.
The access statistics are given below for the primary RCSB PDB website