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Welcome to jV wiki. jV version3 (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 graphics of jV is based on OpenGL JOGL), thereby producing fairly beautiful pictures.
 * jV runs on the Java Runtime Environment (JRE) so that it can work as a stand-alone application as well as an applet.

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 has indicated more detailed explanation and how to use.

-Installation of jV3 is a procedure installed in a local machine.

The old version(jV version1 & jV version2) has not carried out use recommendation.

jV version 3 Outline
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.
 * JRE 1.4.2 or later (recommend 1.4.2_12)
 * 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.