What's New in this Release (November 17, 2009)


Query Results Browser Changes


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.


Improved Tabular Report System


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).

Pagination through the navigation bar

an example of navigation bar

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.

Sorting, hyperlinking, and column resizing

an example of column header

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.

Exporting to other formats

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.


New Advanced Search Interface


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.


Display of Large Structures


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 (e.g. 1JJ2), structures that contain many models of relatively small macromolecules (e.g. 2HYN), and structures that contain multiple models of large molecules (e.g. 1HTQ).

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.

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


Split Entries


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.


Download of Biological Assemblies


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.

Show Example (link to 3IG6 summary page)

We have also updated the tutorial that describes the difference between Asymmetric Units and Biological Assemblies.


Support for CE algorithm in Comparison Tool

Screenshot of an alignment calculated with the new Java version of CE In our previous release we introduced the RCSB PDB Comparison Tool, which calculates pairwise sequence and structure comparisons. You can find it at the left-hand menu under Tools->Compare Structures. The comparison tool is also integrated into the Sequence Similarity report (Show example).

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)

Alignment of Any PDB Files

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 PDB files

Align Custom Files (Launches Java Web Start application)


Show Context of PDB Citations in Literature Report


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 interest.

Show Example Literature Report


New External Widgets


With this release 3 new widgets are being introduced that can be installed and used on any external website.

RCSB PDB Molecule of the Month Widget

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.

RCSB PDB Tag Library

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.

RCSB PDB Image Library

The RCSB PDB Image Library embeds an image of any PDB entry on your website.

Check out more detailed information about widgets here.