jV - interactive molecular viewer

Introduction

PDBjViewer (jV, for short) is a program to display molecular graphics of proteins 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. (Each frame of an animation is made of a single MODEL entity of the traditional PDB format file.)
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.

Basic Usage

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

Action	Mouse Operation
Action	Windows, Linux	Mac OS X
rotate around X (horizontal) axis rotate around Y (vertical) axis	left drag	drag
rotate around Z (anteroposterior) axis	Shift + right drag (move horizontally)	Shift + Command + drag (move horizontally)
translate along X axis (holizontally) translate along Y axis (vertically)	right drag	Command + drag
translate along Z axis (zoom in/out)	Shift + left drag	Shift + drag

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.


Stand-alone (Windows)	Stand-alone (Mac)	Applet

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

Operations	Menu location
Save a static image	[File]-[Save]-[PNG/JPEG]
Change the expression format	[File]-[Display]-[Wireframe/Backbone/Sticks/Spacefill/Ball&Stick/Ribbons/Cartoon]
Change the color	[File]-[Colors]-[Monochrome/CPK/Shapely/Group/Chain/Temperature/Structure/Charge/Amino]

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 the following links for details:

Manual (html in English)
Manual (wiki in English)
Manual (html in Japanese)
Manual (pdf in English, for ver. 3.3)
User's guide (for ver. 3.3 in English)

Graphics Examples


Spacefill expression	Cartoon expression	Molecular surface	Electron density

jV Associates

PDBj Mine: PDB entry search
eF-site: electrostatic surface of Functional-site
P-cats: Prediction of CATalytic residueS in proteins
eProtS: Encyclopedia of Protein Structures

Preparation

To use on web browsers, you need to install the Java Runtime Environment (JRE).
Installing of JOGL is not necessary to use jV version 3.6 or later.

JRE (mandatory)

It is necessary to install JRE version 1.4.2 or later, but this is already installed in many systems. For those systems such as some versions of the Windows OS, download it from Java's official website and install it.

When you use JRE6 Update15 (1.6.0_15) or JRE6 Update16 (1.6.0_16) on Windows or Linux, jV applet and applet-launcher may fail to start up with the following error. So please use JRE6 Update17(1.6.0_17) or later.

	  Error:java.io.IOException:Cannot find certificates for JNLPAppletLauncher class

JOGL (required jV 3.5 or before)

version JSR-231 1.0.0. Download the appropriate version from the following links and install it.

To use jV3 as a stand-alone application, in addition to JRE and JOGL, download and install one of the following:

jnlp file [jV3.8 Java Web Start version (recommended)]
jnlp file [jV3.8 with the latest JOGL]
Executable JAR file [jV3.8]
Source file [jV3.8] (if you ever want to modify and customize the program.)

Documents for applet settings

In case you are to applet settings, you may refer the following documents (PDF file):

[Windows(2007.1.9) | Mac OS X (PPC or Intel) (2006.12.19) | Linux]

Trouble shoooting

When you hit upon some troubles in installing or viewing molecules, refer jV wiki - Trouble Shooting (in English) or jV Usage manual - Trouble Shooting (in Japanese).

Older versions

PDBjViewer (jV)