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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''). Before proceeding, you should be aware that using Java is likely a security threat -- see [[Java#Java_is_a_security_threat |Using Java As Safely As Possible]].
<span style="font-size:130%;"><b>Quick Start</b></span>
* Windows: Use Internet Explorer. Detailed instructions are [[#Internet Explorer in Windows|below]].
* macOS: Use the [https://www.waterfox.net/ Waterfox Classic] browser (not Waterfox Current). In July, 2020, this is the only macOS (11.12 Sierra or later) browser that runs both Proteopedia and [[FirstGlance in Jmol]] with Java. Permission dialogs for using Java are straightforward.
 
To instruct Proteopedia to use Java, add <b>?use=java</b> to the end of the URL in the browser's address line. [[Using_Java_for_Rendering_Structures|Details]].
 
To instruct FirstGlance to use Java, add <b>&java</b> to the end of the URL in the browser's address line.
 
----
Below is explained 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]]).
 
<div style="background:#ffe0e0; width:90%; margin-left:5%; padding:10px">
Oracle, the makers of Java, plans to [https://blogs.oracle.com/java-platform-group/entry/moving_to_a_plugin_free 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. Stand-alone 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.
</div>
 
We believe this page is up to date for '''July, 2020''' (Java 1.8.0_251, [https://www.java.com/en/download/faq/release_dates.xml Java Release Dates]). If you suspect any issues, please email [[Image:Contact-email.png]].
 
==Java Applets do not work in Chrome, Firefox, Edge, or Opera==
 
[https://www.java.com/en/download/help/browser_activate_plugin.xml Official browser compatibility documentation for Java].
 
===Chrome===
[https://java.com/en/download/faq/chrome.xml The Google Chrome browser does not support Java] (including the Java-dependent version of Jmol). This change happened in late 2015 and had been announced well in advance.
 
The HTML5 implementation of Jmol, JSmol, works just fine in Chrome.
 
===Firefox===
[https://www.java.com/en/download/help/firefox_java.xml The Mozilla Firefox browser does not support Java] (including the Java-dependent version of Jmol) since version 52 of the 32-bit browser; the 64-bit Firefox has never supported Java. [https://support.mozilla.org/en-US/kb/npapi-plugins That change happened in March 2017] and had been announced well in advance. Until sometime in 2018, there was a special version of Firefox called ''Extended Support Release'' (ESR) that supported Java; however, [https://www.digitalcitizen.life/how-enable-java-all-major-web-browsers later ESR versions no longer support] Java.
 
The HTML5 implementation of Jmol, JSmol, works just fine in Firefox.
 
===Edge in Windows 10===
The Microsoft Edge browser (new in Windows 10) [https://www.java.com/en/download/faq/win10_faq.xml does not support Java]. However, Internet Explorer 11 is available in Windows 10 for use with Java. See details below.
 
The HTML5 implementation of Jmol, JSmol, works in Edge, although [[User:Eric_Martz/JSmol_Notes#Poor_performance_in_Internet_Explorer.2C_Edge.2C_Chrome_and_Opera|rotation is jerkier and operation is slower than in Firefox or Chrome]].
 
===Opera===
The Opera browser does not support Java.
 
The HTML5 implementation of Jmol, JSmol, works in Opera.
 
==Browsers That Support Java==
[https://www.java.com/en/download/help/browser_activate_plugin.xml Official browser compatibility documentation for Java].
 
 
'''Internet Explorer''' supports Java as of November, 2017. See below for details for each of these browsers.
 
'''Safari''' versions through 11 support Java (through OS 10.11 El Capitan), but [https://www.java.com/en/download/faq/safari.xml Safari 12 and later do not support Java] (OS 10.12 Sierra and later). ([https://en.wikipedia.org/wiki/Safari_version_history Safari Version History]).
 
 
'''[http://palemoon.org Pale Moon]''' (''Windows only'') is an independent browser, [https://en.wikipedia.org/wiki/Pale_Moon_(web_browser) very similar to Firefox], whose developer [http://forum.palemoon.org/viewtopic.php?t=9805 has announced] <u>indefinite support for NPAPI plugins (including Java)</u>, and hence is an alternative to continue running Jmol applets inside web pages, at least while Oracle continues to provide the Java Plug-in.
 
'''[https://www.waterfoxproject.org/ Waterfox Classic]''' (available for Windows and OS X) is very similar to Firefox and supports Java (as of July, 2020, our most recent test). Waterfox is the best solution for macOS.
 
*Waterfox Classic is ''available only for 64-bit operating systems''. It is harmless to download it and try it -- if you have a 32 bit operating system, it won't run. All recent macOS operating systems are 64 bit. Many Windows installations are 32 bit.
<!--
*Waterfox Classic support for NPAPI plugins will presumably end eventually, when the NPAPI code is removed also from the Firefox Extended Support Release (Firefox ESR). The Waterfox maintainers plan to develop a completely new browser with NPAPI plugin support. But even if they can realize it, it will presumably take quite some time until it will be usable. -->
 
'''[http://www.seamonkey-project.org/releases/ SeaMonkey]''' (available for Windows and OS X) is a [https://en.wikipedia.org/wiki/SeaMonkey Mozilla-based browser] that supports Java, at least up to version 2.49.4 current in January, 2019 through July, 2020.
*'''SeaMonkey support for Java has been removed in version 2.53.1'''.<ref>SeaMonkey: NPAPI plugin support. https://www.seamonkey-project.org/doc/npapi (visited 11 June 2021)</ref>
*<font color="red">Seamonkey version 2.49.4 does not run FirstGlance in Jmol. Since all other browsers do, this is probably due to a bug in the javascript of Seamonkey.</font>
 
<!-- Windows 5.1.3.2000 does not work with FG Jmol.
'''Maxthon''' is a browser developed in China. The Windows version 5.0.4.3000 (current through at least November, 2017) supports Java, but concerns have been expressed about data that this browser sends back to China (see [http://www.securityweek.com/maxthon-browser-sends-sensitive-data-china Security Week, July 2016] and [http://www.techrepublic.com/article/maxthon-browser-is-a-wolf-in-sheeps-clothing/ Tech Republic, July 2016] among others). The OS X version 5.0.20 does not support Java.-->
 
==Security with Java==
Before proceeding, you should be aware that using Java is likely a '''security threat''' -- see [[Java#Java_is_a_security_threat |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).
* Safari (OS X): Java is [https://www.java.com/en/download/faq/safari.xml not supported in macOS versions later than El Capitan (10.11)]. If you have El Capitan or earlier: 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).
<blockquote>
If you are using OS 10.6 (Snow Leopard) or earlier, Java is updated through Apple Software Updates.
</blockquote>
 
Use a '''Java-capable browser''': Internet Explorer, Safari, or Pale Moon. (Do not use Chrome, Firefox, Edge, or Opera.)
 
At [http://www.java.com 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.
<blockquote>
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:
[[Image:Safari-trust-java-per-website.png|right]]
 
If you are using the '''Pale Moon''' 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.
</blockquote>
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, '''<font color='red'>pay attention</font> to the pre-checked "recommended" options''' to change some browser preferences. You may wish to '''uncheck''' these. <!--
[[Image:Java-prechecked-ask.png|400px|center]]-->
 
==Enable Java for Web Browsers==
This applies to both Windows and OS X.
[[Image:JavaCP-security.png|right|400 px]]
* 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.
{{Clear}}
 
==Enable Java In Your Browser==
Because Java has a [[Java#Java_is_a_security_threat|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=====
[[Image:Win10 ie search result.jpg|250px|right]]
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:
<ol>
<li> Click Start and type <i>Internet Explorer</i> in the search box. (Do not use Cortana voice commands for this.)
</li>
<li> A "Best Match" list will appear with Internet Explorer at the top (see image at right).
</li>
<li> Right-click on Internet Explorer and "Pin to Taskbar" or "Pin to Start" or both.
</li>
</ol>
 
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.
[[Image:MSIE-view-menu.png|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: [http://bioinformatics.org/firstglance/fgij/fg.htm?mol=1d66&JAVA 1d66 in Java at FirstGlance in Jmol].
{{Template:Unsigned applets}}
 
{{Clear}}
 
 
----
 
===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: [http://proteopedia.org/w/1d66?_USE=SIGNED 1d66 with Java in Proteopedia] (see [[Using Java for Rendering Structures]]).
 
Alternatively, go to [http://firstglance.jmol.org FirstGlance.Jmol.Org], enter a PDB code (a small one is 3hyd), '''check "Use Java"''', and Submit.
 
====Safari 10 in OS X====
The following applies to Safari version 10.x which is current in 2018 in OS 10.10 (Yosemite). If the instructions below don't work, see [[#Safari 11 in OS X]].
 
If the molecule does not display, or you get a <span style='background:yellow;'>yellow message</span> saying that the Java applet is not enabled for this website:
<table><tr><td rowspan="2" valign="top">
# 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.
</td><td>
[[Image:Safari-prefs-security.png]]<center>
Above: Steps 2, 3, and 4.</center><br>
</td></tr><tr><td>
[[Image:Safari-security-websites-java.png]]<center>
Above: Steps 5, 6, 7, and 8.</center>
</td></tr></table>
 
{{Template:Unsigned applets}}
 
====Safari 11 in OS X====
Mac OS 10.11 El Capitan uses Safari 11. We do not have an OS 10.11 test system, but it appears that Java can be enabled in Safari 11 following [https://discussions.apple.com/thread/8361245 these instructions].
 
{{Clear}}
 
<!--====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:
[[Image:Application-blocked.png|center]]
 
 
The following fix applies to both Windows and OS X.
[[Image:JavaCP-exception-list.png|right|400 px]]
* 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...''.
[[Image:JavaCP-exception-list-add.png|400px]]
* 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:
[[Image:Security-warning-unsigned.png|center|450px]]
 
An example of a website using the unsigned Jmol Java applet is [http://higheredbcs.wiley.com/legacy/college/boyer/0471661791/structure/jmol_intro/sec_str.htm Protein Secondary Structure at Wiley.Com].
 
{{Clear}}
 
==See Also==
* [[Java]] which also discusses security.
* [[Using Java for Rendering Structures]] in Proteopedia.
* [https://blokt.com/guides/best-secure-browsers-for-private-browsing The Best Secure Browsers for Private Browsing in 2019]: Chrome gathers as much information about you as it can to send back to Google for marketing purposes. Firefox is not the product of a for-profit corporation, and does not gather such information. This article tells how to maximize your privacy while using Firefox.

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Eric Martz, Angel Herraez, Joel L. Sussman
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