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Welcome to jV wiki.

jV (formerly known as PDBjViewer) is a program to display molecular graphics of protein 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.
  • jV runs on the Java Runtime Environment (JRE) and works as a stand-alone application.
  • The graphics of jV is based on OpenGL (JOGL), thereby producing fairly beautiful pictures.

The program 'jV' has been developed by Kengo Kinoshita (Graduate School of Information Sciences, Tohoku University) and Haruki Nakamura (Institute for Protein Research, Osaka Univeristy), with the support from JST-NBDC and Institute for Protein Research IPR, Osaka Univeristy.

Start up

You can start up jV (4.5.9) with Java Web Start technology immediately from here. Open the downloaded jV.jnlp file.

The current jV requires JRE 1.8 or later.

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
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.

The location of menu in jV stand-alone version in Windows. The location of menu in jV stand-alone version in Mac. The location of menu in applet version.
Stand-alone (Windows) Stand-alone (Mac) Applet

Basic menu operations are following (see also GUI 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 #Other resources for details:


You can also download the program and start it up locally. The following links take you to the download pages. (latest version is 4.5.9@2021/6/28)

Other resources

Contact us

If you have any questions about jV, please feel free to contact us from here.