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

Graphics Examples


Spacefill expression	Cartoon expression	Molecular surface	Electron density

jV Associates

PDBj Mine: PDB entry search
eF-site: electrostatic surface of Functional-site
eProtS: Encyclopedia of Protein Structures

Download & Install

Required environment (use jV as stand alone application)
Required environment (use jV in web browser)
Documents for applet settings
Trouble shoooting

Required environment (use jV as stand alone application)

To use jV as a stand-alone application, in addition to JRE and JOGL same as for using jV in web browser, download and install one of the following:

The Java Web Start version can use the latest version automatically. That is, the update procedure is not necessary, although the Internet connection is required to start this type of jV. On the contrary, the binary files version (jar version) can start without the Internet connection, but you have to update jV manually.

The latest version is 4.5.9.

jnlp file [Java Web Start version (recommended)]
jnlp file [with the latest JOGL] (In case of Mac with Java 1.6, please use this version)
Executable JAR file (For platform with Java 1.5 or older such as former Mac OS, download jV 4.0 from this link)

If you ever want to modify and customize the jV program, please download the source file.

Required environment (use jV in web browser)

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 1.6 or later for jV 4.1, and JRE version 1.4.2 or later for jV 4.0 or older, 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)

The JOGL version JSR-231 1.0.0 or later is required before jV 3.6. Download the appropriate version from the following links and install it. In case of jV 3.6 or later, installing isn't necessary as JOGL is included in the delivery contents. The jV applet is also no need of JOGL pre-installing when the applet page uses applet launcher which download the appropriate type of JOGL automatically.

Documents for applet settings

In case you are to applet settings, you may refer the jV wiki.

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).

PDBjViewer (jV)