jV molecular viewer

PDBjViewer (jV)

[Introduction | Basic Usage | Manual | Graphics Examples | Download & Install | Acknowledgment | jV wiki | PDBj Home ]


Introduction

PDBjViewer (jV, for short) is a program to display molecular graphics of proteins and nucleic acids. jV supports the following features:

Basic Usage

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

ActionMouse Operation
Windows, LinuxMac 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.

The screenshot of the jV application window for Windows The screenshot of the jV application window for Mac
Application window for Windows Application window for Mac

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
Spacefill expression Cartoon expression Molecular surface Electron density

Download & Install

Required environment

To run the jV application, it is necessary to install Java Runtime Environment (JRE) in advance. Please access the Java website to download and install it.

The latest version is 4.5.10.

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

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).


Acknowledgment

The jV program was developed by Kengo Kinoshita (Graduate School of Information Sciences, Tohoku University) and Haruki Nakamura (Institute for Protein Research (IPR), Osaka University) as one of activity of Protein Data Bank Japan (PDBj), with the support from JST-NBDC and Institute for Protein Research, Osaka University.


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