Based on an automatic alignment between UniProt sequences and protein sequences extracted from the PDB structure file other information is mapped onto the structure.

Currently PROSITE motifs, SAPs(SNPs), Pfam domains and the exon structure of the underlying genes are mapped.

The features mapped onto a 3D structure can be highlighted simultaneously.

So you can highlight for example ligands, active sites, SCOP domains, PROSITE motifs, SAPs(SNPs) and mapped exon boundaries within a single view.

The viewer contains Info tables providing details on ligands, active sites, SAPs(SNPs)/variants, PROSITE motifs, exons, SCOP/CATH/Pfam domains and general information on the PDB entry.

The table content of most of the tables is linked to other databases like UniProt, ENSEMBL, PROSITE and SCOP.

The tables are initally hidden and can be displayed by clicking on the Info link beneath the feature name and in the header line.

The asymmetric unit and biological unit files provided by the wwPDB can both be displayed.

Specific color schemes assist in analyzing the differences between asymmetric and biological units.

Automatic standard views are available for highlighting specific features:

Basic interface

Advanced interface

The graphics window (Jmol applet) can be resized freely.

This enables for example to adapt it to your screen size. And it also enables to create high resolution images.
The window size is only limited by the amount of memory available within Java.

In the Jena3D interface all sections can be collapsed/expanded by clicking on the /  buttons.

This enables to customize the interface for the current needs and screen size by hiding unused interface controls.
And a similar mechainism also enables to include large information tables (see above) directly within the interface. They can be shown/hidden by clicking on an Info link.