Installing and enabling Java

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This page explains how to install Java, and how to enable it in various web browsers. Using Java with Proteopedia or with FirstGlance in Jmol will improve performance significantly. Once you have Java working, you can make it the default in Proteopedia (see Using Java for Rendering Structures) or in FirstGlance in Jmol (with its Preferences).

Oracle, the makers of Java, plans to deprecate the Java browser plugin in Java 1.9, and to discontinue the plugin at a future date. Thus we cannot count on the Java plugin indefinitely, but the date when it will stop working is uncertain. Java applications are expected to continue to be supported.

Even before that happens, common browsers are removing the support for running Java applets (like Jmol) within web pages.

We believe this page is up to date for May, 2016 (Java 1.8.0_91, Java Release Dates). If you suspect any issues, please email Image:Contact-email.png.

Contents

Java Applets Do Not Work In Chrome, Edge, or Opera

Chrome

Effective September 1, 2015, the Google Chrome browser no longer works with Java applets (including the Java-dependent version of Jmol). This change was announced well in advance.

The HTML5 implementation of Jmol, JSmol, still works just fine in Chrome.

Edge in Windows 10

The Microsoft Edge browser (new in Windows 10) does not support Java. However, Internet Explorer 11 is available in Windows 10 for use with Java, and Firefox can be installed free. See details below.

Opera

Although the Opera website still talks about installing Java (May 2016), Opera 37 no longer operates the Java plugin, and does not list it on its plugins page even when Java is installed in Windows 10.

Alternatives

Firefox is still supporting the NPAPI interface required for Java, but has announced it will stop doing so at the end of 2016, at least in the standard browser setup. The new 64bit Firefox does not support Java at all.

Internet Explorer and Safari support Java. See below for details for each of these browsers.

Pale Moon is an independent browser, but very similar to Firefox, whose developer has announced indefinite support for NPAPI plugins, and hence is an alternative to continue running Jmol applets inside web pages, at least while Oracle continues to provide the Java Plug-in.

Security with Java

Before proceeding, you should be aware that using Java is likely a security threat -- see Using Java As Safely As Possible. As explained there, Windows users will be safest if they use Internet Explorer for Java, and a different browser, in which Java is disabled, for general web browsing.

Update Your Web Browser

For Proteopedia and FirstGlance in Jmol, Java operates within a web browser (as a "Java applet"). Make sure your web browser is up to date with the latest version.

  • Internet Explorer (Windows): Start, Control Panel, Windows Update (may be under System and Security).
  • Firefox (Windows): Click on the Firefox menu at the upper left (or the Help menu), then Help, then About Firefox, which checks for updates automatically.
  • Firefox (OS X): Click on Firefox in the menubar (top left of screen), then About Firefox, which checks for updates automatically.
  • Safari (OS X): System Preferences, App Store. Click on the Check Now button. Install any available update for Safari or OS X.

Install or Update Java

Start by updating, or installing, Java. The same procedure is used for Windows, or OS 10.7 (Lion), 10.8 (Mountain Lion), 10.9 (Mavericks), 10.10 (Yosemite), or 10.11 (El Capitan).

If you are using OS 10.6 (Snow Leopard) or earlier, Java is updated through Apple Software Updates.

Use a Java-capable browser: Internet Explorer, Firefox, or Safari. (Do not use Chrome, Edge, or Opera.)

At java.com, click on "Do I have Java?". Then click the button "Verify Java Version".

If nothing happens ("Verifying Java" displays indefinitely), click the Download link and proceed to install Java.

If you are using the Safari browser, you may see "Java blocked for this website". Click on that message to get a dialog where you can trust (unblock) Java for this website:

If you are using the Firefox browser, you may see Activate Java Applet. Click on that message to activate. Next you may see a drop-down dialog at the upper left of the browser window that says Allow java.com to run "Java Applet". Click on one of the Allow buttons.

After a brief pause (while the Java Virtual Machine starts), a report will tell you that you are up to date, or that you need to update Java.

If you see "Missing Plug-in" it means that you have no Java installed previously. In that case click Download to download and install Java.

When installing Java, pay attention to the pre-checked options to make Ask.com your default search provider and browser home page. You may wish to uncheck these.

Enable Java for Web Browsers

This applies to both Windows and OS X.

  • Open the Java Control Panel.
    • Windows: Start, Control Panel, Java.
    • OS X: System Preferences, Java.
  • Click the Security tab.
  • Make sure that Enable Java content in the browser is checked.
  • Setting the security level to High is OK.
  • Click the OK button at the bottom.

Enable Java In Your Browser

Because Java has a history of being a security problem, each web browser has controls to enable or disable Java. Typically it is disabled by default, so it must be enabled.


Windows

The instructions below were tested in Windows 10, Windows 7 and Windows XP.

In Windows XP, tests were done with Java 1.7.0_71, 1.8.0_45, and 1.8.0_91. Java 1.8 warns that it is not fully compatible with Windows XP, but it installed OK and afterwards, no problems were seen running the Jmol Java applet in the browsers listed below.

Internet Explorer in Windows

Accessing Internet Explorer in Windows 10

Windows 10 recommends that you use the new Microsoft Edge browser, but it does not support Java. Internet Explorer 11, which supports Java, is included in Windows 10 but is initially hidden. To access it:

  1. Click Start and type Internet Explorer in the search box. (Do not use Cortana voice commands for this.)
  2. A "Best Match" list will appear with Internet Explorer at the top (see image at right).
  3. Right-click on Internet Explorer and "Pin to Taskbar" or "Pin to Start" or both.

Now you have convenient access to Internet Explorer for use with Java applets.

Internet Explorer: Enabling Java

This procedure should work in Windows XP and all later versions including Windows 7 and Windows 10.

  • Right click in a blank gray area near the top of the browser window. A menu should open as shown at right.
  • Make sure that Menu bar is checked.
  • Open the Tools menu (also available from a gear-shaped icon at the upper right of the browser window) and click Manage add-ons.
  • In the window that opens, on the left, select Toolbars and Extensions.
  • In the main list, find Oracle.
  • Click Java (under Oracle) and make sure it is enabled. If there are multiple Javas, enable all.
  • Click the Close button.

Go to a Java-applet requiring website, and after OK-ing two permission dialogs, the Java applet should display the molecule. Here is a link for testing: 1d66 in Java at FirstGlance in Jmol. If the molecule still is not displayed, the website may be using an older unsigned Java applet. This requires one additional step: see Enable Unsigned Java Applets.


Firefox in Windows

  • Open the menu in the upper right corner (or the Tools menu). Image:Firefox-menu.png
  • Click Add-ons.
  • Select Plug-ins in the column at left.
  • Make sure Java is set to Ask to Activate (not "Never Activate").
  • Go to a test Jmol Java applet page: 1d66 in Java in FirstGlance.
  • Click the Allow button in a gray security dialog that appears. (With Java 1.7 in Windows XP, you may need to approve several permission dialogs.)
  • Now you should see the molecule! (If you don't, try simply reloading the page.)

If the molecule still is not displayed, the website may be using an older unsigned Java applet. This requires one additional step: see Enable Unsigned Java Applets.



Apple Mac OS X

Testing the Jmol Java Applet

Proteopedia.Org displays molecules in Jmol. In order to force it to use the Java applet, use this link: 1d66 with Java in Proteopedia (see Using Java for Rendering Structures).

Alternatively, go to FirstGlance.Jmol.Org, enter a PDB code (a small one is 3hyd), check "Use Java", and Submit.

Firefox in OS X

With Firefox in the foreground, open the Tools pull-down menu from the menubar (top of your screen). Select Add-ons. Select Plug-ins at the left, then under Java set it to Ask To Activate. (Always Activate is not a safe setting.)

Now when you go to a website that needs Jmol, you may need to OK up to four permission dialogs before Jmol is allowed to run. Some have checkboxes to remember your choice. If the molecule still is not displayed, the website may be using an older unsigned Java applet. This requires one additional step: see Enable Unsigned Java Applets.

Safari in OS X

If the molecule does not display, or you get a yellow message saying that the Java applet is not enabled for this website:

  • Open Preferences from Safari in the menubar.
  • Click the Security tab.
  • At "Internet plug-ins", make sure that Allow Plug-ins is checked.
  • At "Internet plug-ins", click the button Website Settings.
  • Select Java on the left.
  • You should see Currently Open Websites, probably with the setting "Off" (or "Ask").
  • Change the setting to "On" (or "Allow").
  • Click Done, and close the Preferences.
  • Reload the page that needs the Jmol Java applet.
  • You will likely need to allow several permission dialogs.

If the molecule still is not displayed, the website may be using an older unsigned Java applet. This requires one additional step: see Enable Unsigned Java Applets.

Opera in OS X

Tools, Advanced, Plug-ins, Java, Enable. With Opera version 12.16 (current March 2015 through May 2016) and Java 7 or 8, we have been unable to get the Jmol java applet to display. The lack of any new versions of Opera for more than a year suggests that support for OS X has ended.

Enable Unsigned Java Applets

This step will not be necessary for recently updated websites, such as Proteopedia or FirstGlance in Jmol, that use a Java applet signed by a trusted authority. If you can already see the molecule, you don't need to do this step.

After doing all the above steps, websites that still use the unsigned Jmol Java applet will remain blocked:


The following fix applies to both Windows and OS X.

  • Open the Java Control Panel.
    • Windows: Start, Control Panel, Java.
    • OS X: System Preferences, Java.
  • Click the Security tab.
  • In the section Exception Site List, click the button Edit Site List....

  • Click the Add button, and paste or type in only the domain name of the website, as shown in the examples in the above screenshot. Include http:// but stop before the next slash.
  • Click OK and confirm saving this website.

Now the molecule should display in the unsigned Java applet. You may still need to give permission in a dialog like this:

An example of a website using the unsigned Jmol Java applet is Protein Secondary Structure at Wiley.Com.

See Also

Proteopedia Page Contributors and Editors (what is this?)

Eric Martz, Angel Herraez

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