The Jena3D Viewer (Jena3D) is a web-based interactive molecular viewer for three-dimensional biopolymer structures.

Jena3D provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB).   In addition, local structure files can be viewed.

Jena3D is based on Jmol, an open source Java applet.

Jena3D visualizes not only information included in the PDB files but also SCOP, CATH and Pfam domains, SAPs(SNPs), PROSITE motifs and the exon structure mapped onto proteins.

Jena3D is closely linked to the Jena Library of Biological Macromolecules (JenaLib).


(-) Structure Selection

by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
Upload: OR
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the Jmol documentation for a complete list)
Viewer type:  Jmol [Java applet]   JSmol [Javascript]

(-) Main Features

(-) Mapping of Sequence-Based Information
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.

(-) Simultaneous Display of All Available Mappings
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.

(-) Information Tables
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.

(-) Display of Asymmetric and Biological Units
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.

(-) Standard Views
Automatic standard views are available for highlighting specific features:
Default, Hetero/Site, SNP/Variant, PROSITE, Exon, SCOP, CATH, SCOP + CATH, Pfam.
(-) Switchable Interfaces
Basic interface
designed for convenience
Advanced interface
designed for high flexibility

It can be switched between both interfaces at any time without loosing any work done.

(-) Scalable Graphics Window
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.

(-) Collapse/Expand Mechanism
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.


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