WHAT'S NEW

The April 08, 2014 release offers the following new features:

Structure Validation Reports

Access to Worldwide PDB Validation Reports

Validation Reports in RCSB PDB

A Validation Report slider gives an indication of the quality of the determined structure.

The wwPDB has released Validation Reports for all X-ray crystal structures released in the PDB archive as announced at wwPDB.org. These reports contain an assessment of the quality of a structure and highlight specific concerns by considering the coordinates of the model, the experimental data and the fit between the two. Easily interpretable summary information that compares the quality of a model with that of other models in the archive will help users of PDB data to critically assess archived entries and to select the most appropriate structural models for their needs. The reports implement recommendations of a large group of community experts on validation of X-ray crystal structures and have been developed in the context of a larger initiative, the new wwPDB Deposition and Annotation system.

These Validation Reports are available from the wwPDB FTP. These reports have also been integrated into the Structure Summary pages. The report's "slider" graphic is now visible on RCSB PDB Structure Summary pages along with a link to the Validation Report PDF. For examples, view the Structure Summary pages for 1CBS (1.8 structure of a small protein and a ligand, an entry with better overall quality relative to all X-ray structures) and 1FCC (a 3.2 structure with worse overall quality relative to all X-ray structures).

RCSB PDB Mobile on Android

Now Fully Supported on iOS and Android Platforms

RCSB PDB Mobile on Android

RCSB PDB Mobile is now fully supported as an app for Android and iOS devices. It supports simple queries of the PDB archive, browsing of results, 3D structure visualization, and access to the complete catalog of Molecule of the Month articles.

Chemical Structure Searching Using Marvin JS

Find ligands in the PDB

Marvin JS BTN

The Marvin Sketch Java applet from ChemAxon used for small molecule queries has been upgraded to the Marvin JavaScript (JS) version.

Marvin JS can be used to draw a diagram using the chemical editor tools or to edit a ligand loaded into the editor via ligand ID or SMILES string.

Marvin JS can be accessed from the Chemical Component Search page and from within the Advanced Search Interface (under the Chemical Components section), where it can be combined with other search criteria.

Structure Visualization with JSmol

The JavaScript version of Jmol

JSmol with 4LIW

JSmol view of 4LIW

The Structure Summary 3D View option offers interactive views using either Jmol (Java applet) or JSmol (JavaScript). JSmol is now automatically launched if Java is not detected or if the browser does not support Java applets (e.g., Chrome on Mac). JSmol is also used in all Molecule of the Month articles.

Browser Compatibility Check

What Browser am I Using?

Browser Check

The Browser Compatibility Check can indicate if the current computer settings used can successfully run all RCSB PDB features. This functionality has been upgraded, and now incorporates more sophisticated browser detection using Google's WhatBrowser.org service.

Check your browser now.

Tabular Report Web Services

Easily Export Data

Tabular Report Web Services provide an easy way to export data to a CSV, Excel, or XML file. This service has been extended to allow POST requests to support an unlimited number of PDB IDs (unsupported by GET requests).

Tabular Report Web Services

Code snippet of the Post Query method

Look at a Java example.

Advanced Search for Gene Names

Search PDB by UniProt Gene Names

The new Advanced Search query for gene names can identify all PDB entries associated with a specific UniProt gene name.

Advanced Search for Gene Names

Search PDB for Uniprot gene names