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Welcome to jV wiki. jV(formerly known as PDBjViewer) is a program to display molecular graphics of protein and nucleic acids. jV can use as a stand-alone program and can operate on a web browser as an Java applet. jV is used by PDBj services(eF-site, eF-seek, the molecular structure surface database of the protein functional part).

jV supports the following features:
 * jV can read and display PDBML files, the canonical XML format for the Protein Data Bank.
 * Of course, jV can read and display the traditional PDB format files, too.
 * RasMol-like usability.
 * jV can process more than one molecules.
 * jV can display polygons specified by XML. (XML Schema for polygons is available.)
 * Multiple polygons can be processed simultaneously, and be superimposed onto molecular images.
 * Animation can be realized.

The program 'jV' has been developed by Kengo Kinoshita (Human Genome Center, Insutitute for Medical Science,University of Tokyo) and Haruki Nakamura (Institute for Protein Research, Osaka Univeristy), with the support from JST-BIRD.

jV version 3
jV version 3 is now used to display molecules and their surfaces as a Java applet program. Version 3.6 was released on 11, Aug, 2008. This version is fully compativle with applet-launcher. Go to jV version 3.

It requires the following softwares.

The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.
 * JRE 1.4.2 or later (recommend 1.4.2_12) jV runs on the Java Runtime Environment (JRE) so that it can work as a stand-alone application as well as an applet.
 * JOGL 1.0, 1.1.1 or JSR-231 1.0.0 (recommend JSR-231)
 * version 1.0 [Windows,Mac OS X,Linux]
 * version 1.1.1 [Windows,Mac OS X, Linux]
 * JSR-231 1.0.0 [Windows, Mac OS X ppc, Mac OS X universal, Linux]

Note:  JOGL 1.0 and 1.1.1 are not available for Intel Mac.The latest version of JOGL, JSR-231 1.0.0, runs on Intel Mac.

jV version 2
jV version 2 is an advanced version of PDBjViewer, which can be used only as a stand-alone program. It enables to display more than one molecule images at the same time and their display models and transforms can be operated separately. An animation of molecules can be also performed. jV version 2 runs with .NET framework 1.1 on the Windows platform. Therefore the .NET framework must be installed on your computer.

jV version 1 (PDBjViewer)
Visualization of structure and surface of molecules is performed by a Java applet program called 'PDBjViewer'.

Two image windows are opened. The structure of the molecule is shown in the left window and the molecular surface is displayed in the right window. The mouse control is as follows.

In order to use PDBjViewer, Java Plug-in and Java 3D API must be installed on your computer. The version requirements are as follows.


 * JRE (includes Java Plug-in) 1.4.1 or later (recommend 1.4.2)
 * Java 3D API (OpenGL) 1.2.1 or later (recommend 1.2.1_04)

Important notes
 * 1) You can select two kinds of implementation of Java 3D, OpenGL version and DirectX version. But, PDBjViewer only work with OpenGL version at present.
 * 2) PDBjViewer does not work with JRE from 1.4.1_03 to 1.4.1_06.

PDBjViewer can be used as a stand-alone program as well as an applet with the same requirements as above. In addition to mouse controls, a command line interface is provided.