Trouble shooting

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Latest environment is recommended

Using latest version of Java and jV is recommended to avoid problems. Following issues are known for older versions of them.

  • jV applet fails to start on JRE 1.6.0_15 and 1.6.0_16 by a certificate error.
  • Java's file-cache functionality causes a problem on JRE 1.6.0_15 and 1.6.0_16.
  • jV applet fails to start on JRE 1.6.0_21 because of a conflict with next-generation Java Plug-in.
  • jV of versions eariler than 4.1 do not run as an applet on recent Mac OS.

JRE 1.7 is required on Mac OS 10.7 or later

Apple-provided Java SE 6 does not support Java applets now. The following changes were made at Java 1.6.0_37[1]:

  1. All the java plug-ins for every web browser provided from Apple Inc. will be removed.
  2. The "Java Preferences" application will be removed.

If you access a web page containing a Java applet and click on the region labeled "Missing plug-in", you can go to a download page of JRE 1.7. When JRE 1.7 is installed, you can use Java applets. It is reported, however, that Java Web Start fails to start with JRE 1.7 in some cases, and the issue is not resolved yet.

JOGL library conflict

If you cannot start jV as a standalone program or view jV applets due to a failure of locating the JOGL library, try the followings.

clear cached files

Previously cached JOGL files may be the cause of a problem (on JRE 1.6.0_15 and 1.6.0_16, cached JOGL files conflict with newer files placed on the server). The following steps show how to clear cached files.

1) Open Java Control Panel
In Windows, double-click the [Java] icon located at Control Panel. In Mac OS, click the [Java] icon in System Preferences.
2) Open Java Cache Viewer
On the Java Control Panel, select [General] tab and click [View...] button at the section of Temporary Internet Files, then Java Cache Viewer window appears.
Java cache viewer.png
3) Remove cache files
In Java Cache Viewer, you can switch categories with [Show:] pull-down list. Remove all cache files in [Applications] and [Resources] categories.

In old versions of Mac OS, Java Preferences utility is offered instead of Java Control Panel. In such cases, use Java Preferences as follows.

1) Open the Java Preferences window
Double-click the [Java Preferences] icon, then the Java Preferences window appears. The place of [Java Preferences] depends on the version of Mac OS as following:
Mac OS X version place
10.4 [Applications]-[Utilities]-[Java]-[J2SE 5.0]
10.5 (before installing Java for Mac OS X 10.5 Update 4) [Applications]-[Utilities]-[Java]
10.5 (after installing Java for Mac OS X 10.5 Update 4 or later) [Applications]-[Utilities]
10.6 [Applications]-[Utilities]
The contents of the [Java Preferences] differ for the version of Mac OS. In case 10.4, use the [General] tab, which is default displayed. In case 10.5 or later, click to display [Network] tab.
2) Press 'Delete Files...' button
The [Delete Temporary Files] window, which asks which items are to remove, will be opened.
Javacache del en.png
3) Leave all the checkboxs on and click 'OK' button.
4) In some case, restoring the Java environment to the default may be also required.
To do it, click "Restore Defaults" button in the [General] tab.

remove local JOGL library

Older versions of jV asked users to install JOGL libraries locally; however, manual installation of JOGL is not necessary for recent jV. Locally-installed JOGL libraries of different version cause conflicts with recent distributions of jV and should be removed. JOGL library files are different between operating systems.

Mac OS X

Open the [Macintosh HD]-[Library]-[Java]-[Extensions] folder. If some of the following files

  • jogl.jar
  • gluegen-rt.jar
  • libjogl.jnilib
  • libjogl_awt.jnilib
  • libjogl_cg.jnilib
  • libgluegen-rt.jnilib

exist in the folder, remove them. Here, this operation requires root privilege.


Files that should be removed are as follows.

  • <JRE>\lib\ext\jogl.jar
  • <JRE>\lib\ext\gluegen-rt.jar
  • <JRE>\bin\jogl.dll
  • <JRE>\bin\jogl_cg.dll
  • <JRE>\bin\jogl_awt.dll
  • <JRE>\bin\gluegen-rt.dll

Here, <JRE> denotes the folder that JRE has been installed; typically <JRE>=C:\Program Files\Java\jre6.


Files that should be removed are as follows.

  • <JRE>/lib/ext/jogl.jar
  • <JRE>/lib/ext/gluegen-rt.jar
  • <JRE>/lib/<arch>/
  • <JRE>/lib/<arch>/
  • <JRE>/lib/<arch>/
  • <JRE>/lib/<arch>/
  • <JRE>/lib/<arch>/

Here, <JRE> denotes the directory that JRE has been installed; typically <JRE>=/usr/java/jdk1.6.0_17/jre, and <arch> the processor architecture such as <arch>=i386.

Check the environment variable

In some environment, especially Windows, you can't launch the stand alone jar version of jV. If you fell on such trouble, please check the environment variant includes the path of java.

The name of environment variant
  • PATH
The value that should be added
The path of java(.exe). e.g: C:¥Program Files (x86)¥java¥jre7¥bin

Radio button/Pull down menu to switch displaying manner doesn't work

When you browse jV applet pages such as in PDBj Mine and the radio button or pull down menu doesn't work, please try following procedures.

  1. Close the jV applet page.
  2. Terminate all running Java Applet application.
  3. Open the page again.

The key modifier for mouse drag action is not available in Mac 10.10 + Firefox

Mac 10.10 + Firefox 37.0b1-40.0.3
The modifier is ignored for mouse actions with key modifier such as Shift+drag (zoom in/out) and Command+drag (translate), so the behaviors of these actions are same as simple drag (rotate).

At the date of 26 August 2015, we are waiting for the correction of Firefox. The alternative way to such action with command is available. You can zoom in/out by zoom command and translate by translate command. Or you can use another web browser such as Safari and Opera. The stand alone version is also available.