JUMBO 3.0-J XML-CML molecular browser and toolkit

This distribution contains:

• The complete JUMBO runtime on any Java 1.2/Java3D-enabled platform
• A standalone CML editor based on JME (available for Windows and MacOS X)
• Source code for the jumbo.* libraries
• SimpleCML - an introduction to CML programming: Source code and API Docs
• Documentation of the CORE-CML project
• Selection of test molecules in many formats and with differing information

Setting Up

In order to run the applications on this distribution you will need to install the following before you try any demos:

• Java Runtime Environment 1.3.1 or later. You may download this from the Javasoft site. Required for JUMBO3-JMVS and JME.
• Java3D RTE. Must be downloaded from the Javasoft site. and required for JUMBO3-JMVS (available for Windows and some versions of Unix only). After installing, we recommend you reboot your computer.

Click here [mirror site] (1,864,109 bytes) to acquire and Unzip the distribution. This creates a directory called jumbo3, which contains index.html. You can most conveniently initiate all the demos by opening this file using a Web browser (Netscape or IE). If on Windows you relocate the directory from C:\jumbo3, you will need to change the CLASSPATH appropriately in the .bat file.

On windows you can run JUMBO with cml/src/runBrowser.bat. On UNIX you should set the classpath analogously.

Jumbo 3.0-JS

This is a lightweight version of Jumbo3 written in JavaScript rather than Java, and can be used for reading and displaying for XML/CML files. The CML is converted internally via the DOM (buiIt using JavaScript) into SVG comments, which are passed to an SVG viewer for display. Jumbo3-JS runs on "any XML-aware browser" which at present is MSIE5 or IE6. It also requires an SVG plugin such as the Adobe plugin..

It is destined as an open-source tool for displaying and managing molecular information especially for individual scientists or those collaborating in open programs. Future developments may include data and molecule entry.

The components of the system are:

• The XML-CML engine in Javascript (display.js and individual *.html files)
• A large number of molecules in CML. These have been converted from other formats and this process is not yet validated. There will be many different styles of molecule and JUMBO3 is intended to make the best educated guess as to how to present the information.

The browser is only for display at present, but interactivity will come later. The main screen has four components:

• TopLeft: controls to alter the display (scale, etc.). Mouseover describes each one
• Left: List of molecules. Many have no title other than a reference number. Each molecule is in a separate *.xml file.
• Main display. The molecule is drawn here. 2D molecules (connection tables) are draw if there are coordinates. At present the automatic layout facility is not implemented in Javascript and is run offline. 3D molecules are draw as one of 3 projections (x, y, z). They can be rotated (NOT interactively) by typing a rotation angle into "3D" box. Note that 3D molecules have NO depth-related presentation at the moment and atoms will always overlay bonds. Chirality (wedge/hatch) is extremely misleading and is dubious in "3d" coordinates. The test molecules may not always display. Crystallography is not yet implemented.
• Bottom: annotations. JUMBO3 will pick up titles and comments in XML files.

Use with care. Not all errors have been trapped (i.e. don't try scales of zero!). Have fun.

Start JUMBO3-JS (new window)