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.

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

For the detail, Some examples
 * The reference manual jV3 Manual link:
 * The install manual Installaion of jV3
 * 1) Animation
 * 2) User jV with applet launcher

Release note
Changes and improvements have been made as follows.


 * version 3.1
 * The following commands have been added; 'animrange', 'set adjustview', 'show godata', and 'show xps3'.
 * The xPSSS expression has been added in order to select a group of atoms.
 * Several public methods have been added to the applet so as to append molecule or polygon files after the applet started.
 * The applet can send information about mouse-picked atoms to JavaScript.
 * version 3.1.1
 * Some problems in GUI menu [Options]-[Hetero Atoms] and [Hydrogens] have been fixed.
 * Some problems in 'trace' command have been fixed.
 * version 3.1.2
 * eF-site ID has been changed to a new format.
 * version 3.1.3
 * Some problems in xps3 atom selection have been fixed.
 * version 3.1.4
 * Some problems in finalization process of openGL rendering have been fixed.
 * version 3.1.5
 * The output of 'show xps3' command has been modified.
 * Some problems in 'save png/jpeg' command have been fixed.
 * version 3.1.6
 * Some problems in loading an empty polygon file have been fixed.
 * version 3.1.7
 * Some problems in initialization process of the applet have been fixed.
 * version 3.2
 * 'show site' command has been added.
 * version 3.3 beta 1
 * Availabe JOGL version is restricted to JSR-231 beta 5 only.
 * version 3.3
 * Both the previous JOGL (version 1.1.1) and JSR-231 are available.
 * The following commands have been added; 'set viewpoint', 'show viewpoint', 'set imagesize', and 'show imagesize'.
 * version 3.3.1
 * Some problems in reading a pdbMLplus file have been fixed.
 * version 3.4
 * PDB format version 3 can be processed.