Java Web Start Troubleshooting

Java Web Start works smoothly for most users, still the following sections address some issues that may possibly arise. Let us know if you encounter any problems.
What is Java Web Start?

Java Web Start provides a platform-independent and secure deployment technology. It allows users to start Java applications from a web server. Java Web Start works with any browser. It also makes sure that the application is always on the latest version.

Can't start application
Most probably your browser is not set up in a way so it knows to send the Java Web Start files (.jnlp) to the Web Start application.
  • Your browser/system may not be set to send the Java Web Start files (.jnlp) to the Web Start application. Try downloading the latest version of Java.
  • Your browser/system may block the file RCSB-ProteinWorkshop.jnlp from opening because it is not from an identified developer. Open the Security panel and select "Open Anyway", and then open the file RCSB-ProteinWorkshop.jnlp outside of the browser.
Some of the operating system specific tips are listed below.
My browser displays the .jnlp file as text
Your browser or system is not set up correctly to send .jnlp files to Java Web Start.
    Make sure you have Java installed.


  • In Firefox click on Tool and then Options.
  • Click on the Application tabs.
  • Scroll down the list until you find content type: JNLP File. The select the action Use Java Webstart Launcher.


  • Download the .jnlp file
  • Display the file in Finder
  • right click on it
  • right click on the file => Get Info
  • Open With should show Java Web start. If not, please select it and also click "change all"
  • If you can't find Java Web start on your system, depending on your Java version it is either in
     /System/Library/CoreServices/Java Web
    /Applications/Utilities/Java/Java Web Start
My Java version is too old
  • Make sure you have the latest version of Java installed (see above).
Java Web Start will launch, but returns an error or runs poorly
Our 3D viewers require 3D graphics support. Often out of date or missing video card drivers will prevent the applications from starting or running correctly. To resolve this simply update your video card drivers.
The application wants unrestricted access to my system
All of the web start applications launched from RCSB are downloading PDB files if required. This is technically only possible if you give the application permission to access your system resources. We guarantee that the Java Web Start applications signed by our RCSB digital signature and downloaded from our web site:
  • Are not doing anything harmful or hidden on your system.
  • Have been compiled by our developmental team
  • Are available as open source so you can check the source code.
Opening .jnlp window is displayed
When you try to start an application, a window pops up. Your browsers asks you what to do with the file.
  • In the window, click on Open with, select the javaws executable ( depending on your operating system, the name can be different) and press OK.
  • If the Open with option does not display the Java Web Start executable, you must map the .jnlp file to Java Web Start manually.
    • Open the Firefox preferences, go to the Applications tab.
    • Map the mime-type
      to the javaws executable.
I am using a Proxy for internet connection. Will it work?
Java Web Start should pick up the proxy setting from your browser automatically. Depending on your operating system, your Java Web Start application can contain configuration for proxies as well. Make sure your browser and WebStart are using the same settings. To launch the web start user interface, type javaws.
Learn more on Java Web Start
In order to learn more about Java Web Start please go to the Tutorial provided by Sun.
If your setup is correct, you should be able run the following applications: