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Aquaria Help - Installing on Mac OS
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Installing Aquaria on Mac OS

How to update Java3D?

The most common cause of problems with starting Aquaria on Mac OS is due to using an out-of-date version of Java3D. To update Java3D, please do the following steps. Alternatively, if you are running Safari you can run the Aquaria applet in unsafe mode,.

  1. First, copy and paste the following lines into the Terminal program to remove the out-of-date version of Java3D:

    cd /System/Library/Java/Extensions
    sudo rm j3d* libJ3D* vecmath.jar

  2. Now, open an Aquaria (e.g., click here: Your browser should now automatically install the up-to-date version of Java3D and run Aquaria.

If the Aquaria applet stops working?

The Aquaria applet may stop working after you install system updates from Apple. To fix this, repeat the above four steps.

If the latest Java cannot be installed?

Normally, when you try to start the Aquaria applet it should guide you through steps that will install the latest Java. If these steps fail, you can manually install the latest Java as follows:

  1. First, delete any pre-installed Applet plugin by copying and pasting the following line into the Terminal program:

    sudo rm -r /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
  2. Now, install the latest Java Runtime-Environment (JRE) from here:

Using Safari

Currently, we recommend using the Safari browser to run Aquaria. To install the Aquaria applet, first select a protein in Aquaria (or just click here: Next, open Safari Preferences, go to the ‘Security’ tab, click on ‘Manage Website Settings…’. Then click on ‘Java’ - you should see ‘’ (if not, load an Aquaria page) - to allow the Aquaria applet to properly install itself, select ‘Allow Always’. Finally, either select ‘Run in Unsafe Mode’ or follow the instructions in the section below ‘What if the above does not work’.


Note there is currently a bug affecting Java applets - if you first open a web page containing an applet, then attach a new monitor or data projector and move Safari to the display, the applet freezes. To fix, simply quit and restart Safari.

Using Firefox

On MacOS, Aquaria also works with the latest Firefox and the latest Java. Earlier versions of Java had a bug that caused menus in Java applets to occur far away from where they should - if you see this behavior, please update both Java and Firefox. The first time you use Aquaria in Firefox, you will see a warning like ‘’This plugin has security vulnerabilities. Click here to activate plugin”. To prevent this warning from occurring again, please choose to ‘Always activate plugins from this site’ (click the link for details on how to do this).

On the left of the address bar, there is a security icon to click. Make sure you enable both applets to have access.

Using Chrome

Currently on Mac OS, 64 bit Java applets do not work in Chrome. This should be addressed in a future release of Chrome.