A few usability improvements have been rolled into the query results browser page. The "Display/Download", "Generate Reports" and "Query Options"
dropdown lists are now more accessible. The "Display/Download" menu options operate only on the selected PDB IDs (all by default). As before the
"Generate Reports" pulldown menu includes a list of pre-generated summary reports and links to custom reports and image galleries. Improvements to the
query pagination was also added now displaying page and result information.
A new Tabular Report System that supports very large data sets was implemented. The new system also
provides richer functionality in a more intuitive way. Access to the tabular reports has been
simplified on the query results pages (see above).
The above image is an example of the new navigation bar for
reports. Instead of including all structures in a report on a single
page, reports are now available on multiple, customizable pages. By
default, the first 15 records sorted by PDB ID will be rendered. The
user can page through the report using the navigation bar. There is an
option to list 30, 45, or 60 records per page.
Table sorts can be done on the entire report by clicking the
column headers. Within the reports themselves, PDB IDs link to that
entry's Structure Summary page, PubMed IDs link to the abstract, and
Ligand IDs link to a Ligand Summary page. All column widths are
resizable by dragging the line between two columns.
The report exporting feature has been greatly enhanced. Tables can be exported in three formats:
The Excel spreadsheets have been reformatted with customized column width, text wrapping,
alignment, and hyperlinks on selected columns. Formatting issues with PDB IDs that resemble floating
point numbers such as 1E10 have been resolved.
This release introduces a new Advanced Search interface that allows
users to perform complex queries in an intuitive manner. Multiple
simple queries can be combined into one complex search. Search
criteria are more clearly defined and the search buttons have been
rearranged to make it easier to add and remove search parameters.
We are also introducing a new, more intuitive help system that
will eventually replace our current robohelp system. By default, the
new help system will open in a shadow box interface. Clicking on the
pop-up link will cause help to open in a separate window. The user can
choose whether to keep the default shadow box or always have help open
in a new window.
We have made several enhancements to our Jmol page in order to display large structures.
Previously, some structures with very large coordinate files failed to display
because they would have required more memory than was available to the Jmol applet. We are now able to display
structures that contain a large number of chains
(e.g. 1GAV, see image to the left),
structures that contain very large molecules
structures that contain many models of relatively small macromolecules
and structures that contain multiple models of large molecules
These structures are loaded into Jmol using a version of the PDB coordinate file that includes only
backbone atoms for all polymers (Carbon-alpha atoms for proteins and
phosphate atoms for nucleic acid chains) and all ligands including
waters. All HETATM records are retained and displayed as well. In
addition, for the display of the asymmetric unit, only the first MODEL
from the PDB coordinate file is loaded and displayed (Jmol command: load filename 1).
The display of biological assemblies, however, requires the inclusion of all MODELs.
load filename 1
Users should be aware that even these filtered coordinate files are large
files and hence may take a while to download and display in Jmol (depending on the user's network and computer).
The PDB coordinate files that are limited to CA and P atom traces are available
from the following URLs:
Asymmetric Unit: http://www.rcsb.org/pdb/files/1gav.pdb?traceOnly=yes
Biological Assembly (1): http://www.rcsb.org/pdb/files/1gav.pdb1?traceOnly=yes
A number of structures in the PDB are so large that the historical limitations of the PDB file format
(5 columns for atom numbering, 1 column for chain ID) has required them to be split across multiple
PDB coordinate files. These structures include the extremely large ribosome complexes
(e.g. 1GIX, 1GIY),
and they also include other structures that contains a very large number of atoms or chains, such
as the vault protein featured in the images to the left
(2ZUO, 2ZV4, 2ZV5).
These structures are now prominently identified by the new "Split
Entry" box on the entry's Structure Summary page. This box lists the
PDB IDs of all entries that make up the composite structure, and links
to the Structure Download Tool to easily access the related files in any format.
On the right hand side of the Structure Summary page, the visualization
options have been adapted to accommodate these split entries.
Using the forward and backward buttons, the
image box can be toggled between one or more biological assemblies and
the asymmetric unit (just as in the case of single, non-split entries).
The Jmol link underneath the image toggles accordingly between the
composite biological assembly and the composite asymmetric unit.
The display of such large, composite entries in Jmol was enabled by loading
PDB files limited to CA and P atoms
(see Display of Large Structures above), and
by using the Jmol load files command.
The origin of biological assembly information has been added to
the Download Files menu (A = author assigned biological assembly, S =
software generated biological assembly). A mouse over the biological
assembly file name in the pull-down menu displays additional
information, i.e. the software used to generate the biological
assembly. This information has also been added to the bottom of the
Biological Assembly widget on the structure summary page.
We have also updated the tutorial that describes the
difference between Asymmetric
Units and Biological Assemblies.
With this release, the CE algorithm algorithm has been
incorporated into the Comparison Tool as a stand-alone application via
Java Web Start.
The 3D display shows the alignment of the two selected proteins. If
there are any ligands associated with the chains selected for
comparison, they are displayed in the superimposition as well. The GUI
uses the following rules to support interpretation of the alignment:
In bold are the aligned positions. Colored in orange are the aligned
positions of the 1st structure. Cyan is used for the 2nd structure.
Ligands are always colored in orange/cyan to identify which of the
chains they belong to.
Show Example (4HHB.A vs 4HHB.B jCE)
The application that runs jCE and jFatCat via Java Web start now also supports alignments of custom
user provided PDB files. Since the application runs locally,
calculations can be performed without submitting coordinate files to
public servers. Additional functionality now includes saving and
loading of the alignment information to/from local files.
Align Custom Files (Launches Java Web Start application)
The Literature report, available from any entry's Structure Summary page, currently
displays open-access articles from PubMedCentral that cite that particular PDB ID. In
this release we have added support for viewing the textual context in
which a PDB structure has been cited allowing users to get a quick
overview of the articles and identify any that are of particular
Show Example Literature Report
With this release 3 new widgets are being introduced that can be installed and used on any external website.
The Molecule of the Month widget embeds a Molecule of the Month (MOM)
image on your website and links to that feature. The widget can be
customized to specify width, colors, amount of text show, and which
feature to display. If you do not specify a particular MOM issue , the
widget will automatically use the currently featured structure.
The RCSB PDB Tag Library is a rich markup widget that allows easy tagging
of PDB IDs and keywords on any website. The widget provides enhanced
functionality that automatically links back to RCSB PDB pages. Check
out the example on the left by rolling over any of the underlined
words. Currently 3 different tags are provided: pdb_id_tag
provides an image and link to the Structure Summary page,
pdb_menu_tag for a particular PDB ID with useful links to view
the entry in Jmol, to the Structure Summary Page, and to the PDB file;
and pdb_keyword_tag links to a keyword query results page.
The RCSB PDB Image Library embeds an image of any PDB entry on your website.
Check out more detailed information about widgets here.
RCSB PDB (citation) is managed by two members of the Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC
RCSB PDB is a member of the
The RCSB PDB is funded by a grant (DBI-1338415) from the
National Science Foundation, the
National Institutes of Health, and the
US Department of Energy.