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You can execute basic operations such as rotation and translation with mouse action. Major actions are described in the following table:
|Windows, Linux||Mac OS X|
|rotate around X (horizontal) axis
rotate around Y (vertical) axis
|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):
|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:
|Spacefill expression||Cartoon expression||Molecular surface||Electron density|
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 4.5.4.
If you ever want to modify and customize the jV program, please download the source file.
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.
Error:java.io.IOException:Cannot find certificates for JNLPAppletLauncher class
In case you are to applet settings, you may refer the jV wiki.
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.