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

The program 'jV' has been developed by Kengo Kinoshita (Graduate School of Information Sciences, Tohoku University) and Haruki Nakamura (Institute for Protein Research, Osaka Univeristy), with the support from JST-NBDC and Osaka University.

Start up
You can start up jV (4.2) with Java Web Start technology immediately from here. The current jV requires JRE 1.6 or later. The previous version, jV version 4.0, can run with JRE 1.4 and 1.5.
 * stable JOGL version (recommended)
 * recent JOGL version
 * jV 4.0

Basic Usage
You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:

Operations such as changing display models and colors and saving the image, can be executed with a menu. The location of the menu is at the top of the application window in Windows and at the top of screen in Mac as the stand-alone application. As an applet usage, a popup menu appears by clicking the right mouse button on the display screen, or clicking with a "Command" button in case of Mac.

Basic menu operations are following (see also GUI for details):

To execute more complicated operation such as diplaying some piece of the molecule or changing some part of molecule in another style, use command line operation.

See also for details:

Download
You can also download the program and start it up locally. In this case, installing JOGL is required in advance (see Installation page). The following links take you to the download pages. (latest version is 4.2@2012/3/26)
 * binary (4.2)
 * source code (4.2) (registration will be required)

Other resources

 * Manual (html in English)
 * How_to_use (in this site in English)
 * Manual (html in Japanese)
 * Manual (pdf in English, for ver. 3.3)
 * User's guide (for ver. 3.8.3 in English)