by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  

(-) Introduction

The Jena3D Viewer (Jena3D) is a web-based interactive 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).

(-) Applet Type

The Jmol Java applet that is the basis of Jena3D is available in two versions:
  1. The unsigned applet is the default that is used from QuickSearch result links (see below) and crosslinks from the JenaLib.

    It is not able to read or write any files on your computer.

  2. The signed applet can be selected before loading a structure into Jena3D.
    use signed Jmol applet  use unsigned Jmol applet
    It can read or write files on your computer. This enables to export images in different formats (e.g.: PNG, JPEG, POVRay).

    But this is a potential security risk!. Depending on the configuration of your computer it might be possible that the applet for example reads or replaces system or confidential files.
    So if you don't trust us or the Jmol developers don't use the signed applet!

    Because of the higher security risk the browser will ask you if you really want to trust the signed applet before it is started. If you say "no" the applet will only be allowed to do the same things as the unsigned applet.

The Jena3D interface works fully both with the unsigned and the signed applet.

For the upload function (described in the Loading 3D Structures section below) the file is not read directly by the applet. Instead it is read by the browser and sent to the Jena3D server. The applet then reads the file from the server. This way you have full control over the files that are read on your computer by Jena3D. This procedure is also used because the Jena3D interface is specifically built for each structure that is loaded.

So only if you need the extended export possibilities of Jmol (see the Export section below) the signed applet is required.

(-) Coloring

[sorry, this part is not available yet]

(-) Export

[sorry, this part is not available yet]

(-) Interface

[sorry, this part is not available yet]

(-) Jmol Menu

[sorry, this part is not available yet]

(-) Loading 3D Structures

There are four ways to load a 3D structure into Jena3D:
  1. Enter direcly a structure identifier from the Protein Data Bank (PDB code) or the Nucleic Acid Database (NDB code) into the QuickSearch input field.
  2. Enter a UniProt / PROSITE id or accession number or search term(s) into the QuickSearch input field.
    Select a structure from the search results and click onto one of the Jena3D links 3D3D in the result list.
    Header Line: isomerase
    Hetero Full Name: beta-l-arabinose
    Structure Title: crystal structure of galactose mutarotase from lactococcus lactis complexed with l-arabinose
  3. Select a structure file on your computer that should be uploaded into Jena3D.
    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)
  4. By default the asymmetric unit file of a PDB entry is loaded into Jena3D.
    In the menu at the top of the interface you can choose between all available asymmetric and biological unit files for a specific PDB entry.

(-) Rendering

[sorry, this part is not available yet]

(-) Scripting

[sorry, this part is not available yet]

(-) Search

Detailed information on the QuickSearch option is available on the JenaLib QuickSearch Help page.
A quick introduction is presented in the Loading 3D Structures section above.

(-) Selection

[sorry, this part is not available yet]

(-) System Requirements

[sorry, this part is not available yet]