PDBjViewer (jV)

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.
• The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.

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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
	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.

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:

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Manual

• English, html version
• English, wiki version
• Japanese, html version

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Graphics Examples

Spacefill expression	Cartoon expression	Molecular surface	Electron density

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Download & Install

• Required environment
• Trouble shoooting

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