JMV FAQ
JMV Frequently Asked Questions
Table of Contents
1. About JMV1.1 What is JMV?
1.2 What do I need to run JMV?
1.3 Why should I use JMV?
1.4 Who makes JMV?
1.5 Where can I get JMV?
2. Starting with JMV
2.1 What mouse controls are there in JMV?
2.2 What kind of files can I load in JMV?
2.3 How do I run JMV as a standalone application?
3. Installation
3.1 What do I need to install to run JMV?
3.2 I try to run JMV, but it says "Plug in not found". What do I do?
3.3 The Plug-In runs, but the applet window says it can't find Java3D
3.4 For Windows, which version of Java3D should I download?
4. Exceptions and Errors
4.1 I installed Java and Java3D, but I still get an error: "java.lang.NoClassDefFoundError: com/sun/j3d/utils/applet/JMainFrame".
4.2 I tried loading a molecule, but got a message saying there wasn't enough memory.
4.3 I tried switching representations, but got a message saying there wasn't enough memory.
4.4 I tried loading a molecule, but got a message saying it couldn't be found.
4.5 I tried loading a molecule, but got a message saying I didn't have permission to access the file.
4.6 I just downloaded and installed Java, but I got a message saying that the plugin could not be found.
4.7 I just downloaded and installed Java and Java3D, but when I load a molecule, the cylinders are rotated the wrong way.
4.8 I just started JMV, but the dropdown menus won't drop down.
4.9 When I save a jpeg on Windows, the picture isn't getting saved properly.
4.10 When I reload a page running JMV, I get a long error message starting with: "Unexpected signal:"
4.11 JMV says it cannot find Java3D, even though I have it installed.
4.12 I installed Java3D, but it gives me an UnsatisfiedLinkError saying: "J3D.dll A device attached to the system is not functioning"
1. About JMV
1.1: What is JMV?
1.2: What do I need to run JMV?
1.3: Why should I use JMV?
1.4: Who makes JMV?
1.5: Where can I get JMV?
(Note:In the following text, <version-number> refers to the most current version of JMV. For example, for version 0.80, jmv-<version-number>.applet.tar.gz would be jmv-0.80.applet.tar.gz)
jmv-<version-number>.applet.tar.gz: The Unix version of the applet. It contains 3 files:
Extract the files with the commands:
jmv-<version-number>.applet.zip: The Windows version of the applet. It contains 3 files:
Extract the files with WinZip.
jmv-<version-number>.src.tar.gz: The source code for JMV. It contains source code, benchmark applications, sample molecules, applet files, and the makefile for developers to develop with JMV on their own.
2. Starting with JMV
2.1: What are the mouse controls in JMV?
2.2: What kind of files can I load in JMV?
2.3: How do I run JMV as a standalone application?
Download the applet distribution, (jmv-<version-number>.applet.tar.gz or jmv-<version-number>.applet.zip for windows, where <version-number>is the current version number for JMV) and run the command:
3. Installation
3.1: What do I need to install to run JMV?
3.2: I try to run JMV, but it gives me an error saying: "Plug in not found". What do I do?
3.3: The Plug-In runs, but the applet window says it can't find Java3D
3.4: For Windows, which version of Java3D should I download?
3.5: I installed Java3D, but it gives me an UnsatisfiedLinkError saying: "J3D.dll A device attached to the system is not functioning".
4. Exceptions and Errors
4.2: I tried loading a molecule, but got a message saying there wasn't enough memory.
4.3: I tried switching representations, but got a message saying there wasn't enough memory.
4.4: I tried loading a molecule, but got a message saying it couldn't be found.
4.5: I tried loading a molecule, but got a message saying I didn't have permission to access the file.
4.6: I just downloaded and installed Java, but I got a message saying that the plugin could not be found.
4.7: I just downloaded and installed Java and Java3D, but when I load a molecule, the cylinders are rotated the wrong way.
4.8: I just started JMV, but the dropdown menus won't drop down.
4.9: When I save a jpeg on Windows, the picture isn't getting saved properly.
4.10: When I reload a page running JMV, I get a long error message starting with: "Unexpected signal:"
4.11: JMV says it cannot find Java3D, even though I have it installed.
4.12: I installed Java3D, but it gives me an UnsatisfiedLinkError saying: "J3D.dll A device attached to the system is not functioning".
Please direct any other questions or comments to jmv@ks.uiuc.edu.
JMV is the Java Molecular Viewer from the Theoretical Biophysics Group at the University of Illinois. It uses Java and Java3D technology to provide a platform-independent way of viewing molecular structures.
To view JMV in a web browser, you need to install Java Runtime Environment which provides the Java Plug-In, and also Java3D. See the installation instruction page for more information. Once these are installed, you may view the demo or download the demo applet or source code for yourself.
JMV uses Java and Java3D technology, making it platform independent. It can run within a web-browser, and the display is customizable. If this is what you need in a molecular viewer, JMV may be for you.
JMV is created and maintained by the Theoretical Biophysics Group at Beckman Institute at the University of Illinois. The developers are Michael Bach, Robert Brunner, John Stone, and Kirby Vandivort. Please email jmv@ks.uiuc.edu to contact the JMV development team.
JMV samples are available for download from http://www.ks.uiuc.edu/Research/jmv/jmv-0.8/. You can download a sample applet, which includes an html file, a jar file, and a readme file. You can also download the source code. The files you can download are:
jmv-<version-number>.jar: The jar file containing the class files needed by the applet
JMV.html: the html file
README.TXT: a readme file
gunzip jmv-<version-number>.applet.tar.gz;
This will create a directory called jmv-<version-number> containing the 3 files mentioned above. Test JMV by opening JMV.html in a browser.
tar xvf jmv-<version-number>.applet.tar;
jmv-<version-number>.jar: The jar file containing the class files needed by the applet
JMV.html: the html file
README.TXT: a readme file
This will create a directory called jmv-<version-number> containing the 3 files mentioned above. Test JMV by opening JMV.html in a browser.
Extract the files with the commands:
gunzip jmv-<version-number>.src.tar.gz;
This will create a directory called jmv containing the source code directories.
tar xvf jmv-<version-number>.src.tar;
Left button: Rotate
Middle button: Zoom (Up->Zoom Out; Down->Zoom In)
Right button: Translate
Note: On 2-button mice, Zoom is accomplished by holding the Alt key and using the Left button.
JMV currently reads PDB files, although expansion for more types of files is planned. Using the "Load a file" button, you may load files from a URL, from your local disk, or from the RCSB site with a 4-digit code. Note: To load files not on the applet's host, the applet must be signed. For more on signing applets, see here.
java -classpath path/to/jmv-<version-number>.jar JMV
where "path/to/" is the path to the jar file.
To view JMV in a web browser, you need to install Java Runtime Environment which provides the Java Plug-In, and also Java3D. Linux users can download Blackdown's implementation of Java3d here. See the installation instruction page for more information.
To view JMV in a web browser, you need to install Java Runtime Environment which provides the Java Plug-In. Note: You need to have administrator privileges when installing Java in order for the Plug In to be recognized by the browser.
The browser cannot find Java3D. See Sun's Java3D download site to download Java3D for Windows and Unix, or Blackdown's site for Java3D for Linux.
To run JMV, you only need to download one of the JRE versions, not the SDK. For Windows, there are 2 different versions of Java3D. One is the OpenGL version, the other is the DirectX version. Either one should suffice, although different graphics cards may give different performances depending on which you download. See a comparison between the two at j3d.org here for more information.
Make sure that Java3D is properly installed. On Windows, if the DirectX version of Java3D is installed but DirectX is not, it may produce this error. You may wish to install the OpenGL version instead.
4.1: I installed Java and Java3D, but I still get an error: "java.lang.NoClassDefFoundError: com/sun/j3d/utils/applet/JMainFrame".
This often occurs when Java3D is not installed with the version of Java that the browser is using. When there is more than one version of Java installed, Java3D may not get installed with the right one. This can usually be fixed by uninstalling previous versions of Java, and reinstalling Java and Java3D. Or, you can change the path that the Java Plug-In uses for its Java path.
Start the Java Plug-In Control Panel (with the command "ControlPanel" on Suns). In the "Advanced" tab, the "Use Java Plug-In Default" will probably be selected by default. If the dropdown box has a more specific choice, try selecting that. If more than one path appears, select a JRE that has Java3D installed on it. Click "Apply" and try running JMV again.
If a molecule is too large, the Java Virtual Machine may not have enough memory to create it. If the representation is very memory intensive, such as Bonds or CPK, it may not have enough memory to create the representation. In either case, JMV will give you an error message, and attempt to revert the scene to the last known molecule and representation. If the recovery attempt fails, it will notify you again and clear the screen. You may change the amount of memory in the Java Virtual Machine for your browser by running the Java ControlPanel, and adding the parameter "-Xmx[n]", where [n] is the size of the memory to allow. If n ends with "k", the number is in kilobytes. If n ends with "m", the number is in megabytes.
If a representation is very memory intensive, such as Bonds or CPK, it may not have enough memory to create the representation. In either case, JMV will give you an error message, and attempt to revert the scene to the last known molecule and representation. If the recovery attempt fails, it will notify you again and clear the screen. You may change the amount of memory in the Java Virtual Machine for your browser by running the Java ControlPanel, and adding the parameter "-Xmx[n]", where [n] is the size of the memory to allow. If n ends with "k", the number is in kilobytes. If [n] ends with "m", the number is in megabytes.
Double check the URL, code, or file path you entered. Make sure the path is correct and spelled correctly.
In order for an applet to access files that are not on its host server, the jar file must be signed. See here for more information on signing jar files.
If you are using Netscape, try restarting Netscape twice. This is due to a Plugin related bug with Netscape. Also, for Sun and Linux users, make sure that the NPX_PLUGIN_PATH environment variable is set correctly. Do this with the command:
For Sun:
setenv NPX_PLUGIN_PATH <path-to-jre>/plugin/sparc/ns4
For Linux
setenv NPX_PLUGIN_PATH <path-to-jre>/plugin/i386
where <path-to-jre> is the full path to your Java Runtime Environment directory.
This has been seen on occasion. Restarting your computer should fix the problem.
We're not sure what's causing this, but to fix it, just move the browser window. The menus should drop down then.
On Windows, the canvas on which the molecule is displayed must be completely in view and unobscured. If there is another window over the canvas, the window will be in the jpeg. If the canvas is not fully shown in the browser, only the part that is displayed will appear in the browser.
This happens when reloading a page with JMV. This often causes an error in Java, so please try to refrain from reloading a page running JMV.
Start the Java Plug-In Control Panel (with the command "ControlPanel" on Suns). In the "Advanced" tab, the "Use Java Plug-In Default" will probably be selected by default. If the dropdown box has a more specific choice, try selecting that. If more than one path appears, select a JRE that has Java3D installed on it. Click "Apply" and try running JMV again.
Make sure that Java3D is properly installed. On Windows, if the DirectX version of Java3D is installed but DirectX is not, it may produce this error. You may wish to install the OpenGL version instead.
