Overview

A visualization tool:

The MICE structure viewer is designed to be a simple but powerful tool for visualization of complex macromolecular structures. Many of the common styles for representing molecular structures are supported and plans exist to include support for features such as electron density maps and contoured surfaces in future versions.

Scene generation:

MICE uses VRML as the format for transporting molecular scenes. The application can load a scene from a VRML file, which may be stored either on local disk or on a remote webserver. In addition, MICE can generate geometry internally, using the rendering interface and a server-side geometry generator which can read directly from the Protein Databank. Simply by specifying the PDB ID code, a user can generate a customized representation of any available PDB entry.

Interactive structure display:

After generating a molecular scene, tools exist to allow the user to manipulate and query the scene. The user can also opt to distribute their current scene and camera view to other MICE users on the network. This network could be a local ethernet with all users being in the same building, or any larger network, even up to the worldwide internet. Users may “subscribe” to a “published” scene, and will be able to watch the scene move in real time, as another user manipulates it.

Installation

The MICE application is currently available as a standalone application to run on standard desktop computers ¹. MICE enables users to generate complex representations of structures in the Protein Databank via a simple graphical interface.

MICE is written entirely in Java^TM, Sun's platform-independent, network-savvy programming language. To use MICE on any computer, Java and its graphics extension, Java3D, must be installed. All Java components are entirely free and can be obtained via the links to the Sun websites below. Installation should be as simple as double clicking an icon in your file browser.

Like most computer technologies, Java is still evolving and you need to make sure that your machine has a fairly recent version of Java installed. MICE requires Java 2 (JRE version 1.2 or newer) and the Java3D extensions. If in doubt, you may want to re-install everything according to the instructions below ².

Important ! MICE is very much a work in progress and to improve both the application and these instructions, we would like to hear from anyone who's using MICE. There are no restrictions on downloading the application, but please take a moment to drop us a line and tell us that you grabbed it. We will probably be able to help with most installation problems, but only if we know about them. Thanks.

Notes:

1. Subsequent versions of the Java language will include improved support for running programs such as MICE within existing web browsers, removing the need for users to download and install Java manually and making MICE completely and transparently web-deliverable. Back
2. These instructions apply to mainly to the Windows operating systems. There are some pointers for installing Java and mice on other platforms but you should also refer to documentation and websites related to the Java distribution that you're using. Back

Installing Java

• Download Java Runtime Environment (JRE): The Java Runtime Environment is the package which actually lets you run java programs on your machine, just as if they had been written and compiled specifically for your platform. The framework, user interface, networking and collaboration components of MICE are written using pure Java.

  Download the JRE from Sun. Be sure to select the Production Release of Java 2 (version 1.2 or greater) for your platform. At time of writing the release version of JRE from Sun is available only for Windows (95/98/NT), Solaris or Linux. You will need to accept to Sun's licensing agreement before you are allowed to actually download the JRE. You can also download Java 2 for Irix from the SGI website (in SGI's proprietary "tardist" format).

• Install JRE:
  • Windows: To install Java under Windows, use the Windows file browser to locate the installer program that you just downloaded. Double click the installer icon:
    Installation will, by default, install the JRE under your "Program Files" directory. You can change this location if you prefer, but if so you will need to make a small change to one of the MICE files after installation.

    The installer program may recommend that you restart your computer after installation, but you may want to wait until you've installed the other Java and MICE components before restarting.

  • Other platforms¹: On other (unix) platforms, refer to the installation instructions accompany the tar-file that you downloaded. For gzipped tar files, the installation process is normally as simple as unpacking the installation in an appropriate place, but may also require the setting of some environment variables. On SGI, tardist packages may be installed using the standard Irix software management tools. You should not need to restart your computer in order to start using Java.

Notes:

1. MICE is developed using the Sun JDK, running on the Windows NT platform, and tested under Windows NT and Sun Solaris. Although we have successfully run MICE on Linux and Irix, it has not been rigorously tested using the Java environments for these platforms and problems may still exist. Back

Installing Java3D

• Download Java3D toolkit: The Java3D toolkit is an extension to the basic Java environment that adds sophisticated graphics capabilities to the Java language. The three-dimensional graphics which display the molecular scene are created and manipulated using Java3D.

  Download Java3D from Sun. Select the Java3D Runtime for the JRE for your platform. Again, you will be required to accept Sun's license agreement before being allowed to download. Currently only Solaris and Windows versions of Java3D are available directly from Sun, but versions also exist for Linux and SGI. The Linux port of Java3D may be downloaded from one of the Blackdown Java project mirrors, while the Irix version can be obtained from the same site as the JRE.

• Install Java3D:
  • Windows:Locate the installer program that you just downloaded, using the Windows file browser. Double click the installer icon:
    Follow the instructions in the installer. The Java3D installer will try to put the Java3D files inside the existing Java directories. If these are not found in the default location you may need to point the installer program at the correct location when prompted.

  • Other platforms: Again, on platforms other than Windows, refer to the installation instructions accompanying the Java3D package that you downloaded. Installation from a tar archive simply involves unpacking into the same directory as the JRE. Irix tardist packages can be installed using the standard software management tools.

Installing MICE

• Download MICE installer: The MICE application consists of a set of Java class files, which are separate components of the application, broken up into lots of individual files. These class files are stored in “jar” files, which are analgous to “zip” or “tar” files. Finally, to make it easy to install these jar files, MICE is supplied as a Windows executable file, which, when run, unpacks its contents into a folder on disk.

  Download MICE from SDSC. The MICE distribution is currently available as a self-extracting archive for use under windows, as a zip file, for use under either windows or unix, or as a gzipped tar file for use under unix. The three archives all contain exactly the same set of files.

• Install MICE:
  • Windows: Locate the MICE installer that you just downloaded, using the Windows file browser. Double click the installer icon:
    You'll be asked which directory you would like to install MICE in. You can safely install MICE under the Program Files folder - the installer will create new folder there called “Mice”.

  • Other platforms: To use MICE under other (unix) platforms you can either run the MICE installer on a Windows machine to unpack the contents and then transfer them to your intended platform, or, preferably, you can download the files as a "tar" archive.

Running MICE

• Windows: Double-click the batch file.
  • Find the directory in which you just unpacked the MICE installation:
    
  • This folder contains everything that was in the MICE self-installing archive, including the batch file which you use to run MICE. Open the folder and find the file called mice:
    
  • This is an MS-DOS batch file which will start MICE. Simply double-click the icon and MICE should start running. If you didn't install the Java and Java3D files in their default locations, remember to read the instructions on configuring MICE.

• Other platforms: Execute the shell script.
  • To run MICE under unix you will need to write a short shell-script. An example script can be found in the tar file. You should modify this script to point to the correct location for your Java runtime files, including the java executable and the Java3D class files. See the documentation for your platform for more information on how to configure your Java installation.

  • Once you have configured the shell script, you should be able to run MICE by simply executing it with:

    % mice.sh

MICE team Last modified: Fri Nov 3 13:07:33 PST 2000