How to use

jV is an interactive 3D viewer program to visualize protein and nucleic acid molecules. The program reads in a PDBML file that is an XML format for PDB. Usual PDB format files are also accepted. More than one molecule files can be opened and displayed at the same time and their display models and transforms can be operated separately. In addition to molecule files, a polygon file written in XML can be read and displayed. More than one polygon files can be opened at the same time and superposed on molecule images. The XML schema of the polygon file is available. jV can perform an animation of molecules. The animation file is a PDB format file in which each frame is separated by a MODEL line.

jV runs on Java Runtime Environment (JRE) and can be used both as a standalone program and an applet. The 3D rendering is performed with the use of JOGL API. The version requirements are as follows.


 * JRE (includes Java Plug-in) 1.4.2 or later
 * JOGL 1.1.1 or JSR-231

Here, Java Plug-in is required in order to use the program as an applet.

The program allows an interactive mouse control and command execution. The commnad syntax follows that of Rasmol with some modifications. In order to handle the transform of each molecule and polygon separately, every files are set to be either selected or not selected. The transform operation commands, such as rotate or translate, act only on selected files. On the other hand, every atoms in a molecule are also set to be either selected or not selected independently of whether the molecule itself is selected or not selected. Only selected atoms are the target of display model operations, such as wireframe or spacefill commands, and coloring operations.

Release note

How to use
The following table shows hot to do the minimum things with jV.

For the detail,


 * The install manual
 * Installaion of jV3
 * The reference manual
 * User's Guide [[Media:JV3_User'sGuide.pdf|pdf(30 October 2006)]]
 * 1) Tutorials
 * 2) GUI
 * 3) Document type of the polygon file
 * 4) Functional site information for molecules
 * Manual [[Media:JV_manual.pdf|pdf(30 Octover 2006)]]
 * 1) Command List
 * 2) Atom Expression
 * 3) Vertex Expression
 * 4) Color Expression
 * 5) Use as Applet


 * Some examples
 * 1) Animation
 * 2) User jV with applet launcher