Welcome to MollyCule!

MollyCule is a free Open Source Chemistry visualisation program for MacOS, Linux and Windows. MollyCule is designed to be an easy to use program to help ordinary people who want to explore Chemistry.


MollyCule has many simple, fun and easy to use features that make it perfect for teenage scientists and students.

Traditionally, chemistry visualisation packages have used keyboards or complicated mouse-gesture systems to allow you to view molecules from different angles and positions. That's not fun!

In MollyCule, you simply point, click, and go!

MollyCule does all the hard work of figuring how to look at molecules, and flies you around the molecule with animation.

MollyCule can produce animations automatically in real-time, that are very suitable for using alongside a powerpoint presentation or as a backdrop to a class or simply for fun at home. You can also use MollyCule as a screensaver, with the built in 'Drifter' mode.

MollyCule has a special "plug in" design, which means you can easily use and configure MollyCule in any way you like.

You can download molecules from the web, store them or disk, view them as different kinds of model, and light and colour them any way you like.

It's simple to produce beautiful pictures for reports and essays using MollyCule. Just set the picture up the way you like, and save it as a PNG or JPG. You don't need to understand any complicated chemistry, and you don't need to be clever with computers to use it. There's a simple control panel, and no complicated menus to remember. Best of all, MollyCule has a flexible yet straightforward system for lighting.

It's all easy, and if you like programming, you can easily write your own plug-ins to add new features!

MollyCule is completely free for download. Both the program and the source code are contained within the download packages on this site.

MollyCule uses Java and Java3D technologies. Click here for install instructions.

MollyCule is easy to program and extend, too. The code is freely available to make it easy for you to add new Plugin features without having to change the main program.

Almost every aspect of MollyCule can be changed using Plugins - even the user interface could be completely replaced with your own design!

Anyway, I hope you like the sound of MollyCule enough to give it a try. If you like it, please tell other people about it. Remember, you are welcome to give away copies of this program to your friends or students for free. Have fun!

MollyCule for MacOS X
MollyCule for Linux
MollyCule for Windows
Important notice for Windows users - click here!

MollyCule uses Java and Java3D technologies.

You need to read these instructions to install Mollycule.

Click on any atom, and you will fly through the molecule to view it automatically with the new "Point and Go" approach to Chemistry!

Choose different forms of visualisation...

You can temporarily expand the interaction area...

..and go full-screen!


If you're writing an essay or report and want to talk about MollyCule, you are welcome to use this reference at the end of your essay.

"MollyCule", by Graeme Bell, 2000-2010 (http://mollycule.graemebell.net).

Parts of MollyCule are reused from JMVS, JPEGEncoder and PNGEncoder software, under license. Thanks to these people for helping to make MollyCule possible!

This page & images, Copyright Graeme Bell 2010. You are free to re-use these images for any purpose. Please consider adding a link to this site from your own page.

This software was originally developed while I was a student at The University of St Andrews.

Thanks to: S. Walker for feedback and beta testing.