Java - MolProbity Help Java help You do not appear to have Java installed. You will not be able to use the KiNG interactive graphics in MolProbity. Click here to install Java for your browser. If you can see a version number above, you have Java installed. If you see a coffee cup, an animated star, or the like, just wait a minute for the applet to finish loading. If you don't see anything, or just see an error message, keep reading to learn how to get Java. For those in a hurry: get Java now! What is Java? Java is a technology originally developed by Sun Microsystems and now developed and hosted by Oracle that allows you to run small programs, called applets, inside your web browser. Who can use Java? Almost anyone with a reasonably modern web browser can use Java. Most browsers, like Microsoft Internet Explorer, Safari, Netscape Navigator, Mozilla, and Firefox, use the Java Runtime Environment (JRE) provided by Oracle. This is sometimes called a "plug-in". You may already have Java available on your computer -- Macintosh OS X comes with Java built-in (version 1.6.0 as of Sept. 2013), and Netscape Navigator 6 includes Sun's JVM as part of the browser package. Most Windows computers do not come with Java installed, but don't worry -- it's easy to do it yourself. How do I get Java? You may already have Java! If you've used MolProbity before and been able to see the interactive 3-D graphics in KiNG, you have Java. Or, check the message at the top of this page. If you don't have Java or your version is too old, read on. for Windows and Linux: Try going to this page (http://java.sun.com/getjava/) to quickly obtain the latest version of Java. Sun has tried to make it easier, particularly for Windows users, but if you have trouble, come back to this page and keep reading. for the Macintosh: If you have a Mac running OS X, you have Java. Break out the champagne! In rare circumstances, you may have trouble getting Java to work in your browser. If you have trouble, come back to this page and keep reading. Mac OS 9 and earlier do not support modern versions of Java at all -- sorry. Help! It didn't work... for Windows: If you don't already have Java, go to www.oracle.com and download the Java SE Java Runtime Environment (JRE). We recommend getting the newest version (Java SE 7u40 as of September 2013). When prompted to save the file or open it, choose "Open" and follow the instructions that appear. Or, save the file and run it later, following the instructions it displays. IE, Netscape, Mozilla, and Firefox should now make use of Java automatically, without further configuration. If you're running something else, consult that browser's documentation. Sorry! for Linux: If you don't already have Java, go to www.oracle.com and download the the Java SE Java Runtime Environment (JRE). We recommend getting the newest version (Java SE 7u40 as of September 2013). Get either the RPM (RedHat) or the GNUZIP/Tar (any Linux) shell script, save it to disk, and execute it. For the GNUZIP/Tar script, make sure you're in the directory where you want Java installed before running it -- e.g. /usr/local. Sun provides more detailed instructions, but it should be straightforward. The browsers will generally not use Java automatically; they have to be told about it in an additional step. For Mozilla (and Firefox), do something like ln -s /usr/local/jre/plugin/i386/ns7/libjavaplugin_oji.so /usr/lib/mozilla/plugins/ as root. Older Java installations (1.4.x) use /usr/local/jre/plugin/i386/ns610-gcc32/libjavaplugin_oji.so instead. Setup for Firefox should be similar, but using /usr/lib/firefox/plugins/ instead. Java is broken in Konqueror 3.0 as of this writing. If it worked, you would go to Settings | Configure Konqueror... | Konqueror Browser | Java and set the path to Java executable to something like /usr/local/jre/bin/java, depending on where Java is installed. For other browsers, you're on your own -- but you're smart enough to use Linux, you can figure it out. for the Macintosh: The current version of OS X (Mountain Lion 10.8.4) comes with a system Java 1.6.0 installed, but does not include a browser plugin. To install a browser plugin, you'll need to go to www.oracle.com and download the the Java SE Java Runtime Environment (JRE). We recommend getting the newest version (Java SE 7u40 as of September 2013). NOTE: The latest plugin version (1.7.0 as of September 2013) is only available as a 64-bit plugin. Google Chrome is only available as a 32-bit application for OS X, so this plugin is not compatible. Please use Safari or Firefox with MolProbity on OS X. What is KiNG? KiNG is a Java applet and application for displaying 3-D graphics, like macromolecular structures. It implements many of the features found in our primary display program, Mage (coded in C). Why does MolProbity use Java? Java allows our users to view 3-D information in custom software (KiNG) without having to download, install, and configure that software manually. While for some users there is a "startup cost" in obtaining Java in the first place, that one-time cost is effectively shared by the many scientific sites that use Java. For instance, both the Protein Data Bank (PDB) and the Electron Density Server (EDS) offer Java viewing software. Plus, Java is a great language for rapid program development, with a rich set of libraries and extensive documentation (check out the computer books wall at your local bookstore). The same code runs on many types of computers, which reduces our maintainance burden and allows us to spend more time creating features (and, oh yeah, doing science). How much does it cost? Nothing -- Sun gives Java away for free. Is is safe? We believe Java is a very safe way of running programs over the Net, and many protections are built into Java to prevent applets from making changes to your machine. That said, no piece of complex software (like Java or KiNG) can be guaranteed to be free from bugs and potential vulnerabilities. All use of this site is at your own risk. User manual home | Tutorial home | About the Richardson Lab
