This file is very important. You must follow these steps if you want to 
run MollyCule on Windows or Linux. MacOS X users can choose what to do.

---- Short version ---

Step 1: Install Java. Install Java3D. 
Step 2: Install and set-up MollyCule. 
Step 3: Run MollyCule and have fun!

---- Long version ----


Step 1: Java and Java3D are already installed in Macos X 10.5 and 10.6, but not 
in MacOS X 10.7 (Lion) or later. If you have an old version of MacOS, 
you don't need to do anything here. However, if you are running Lion or 
later, you will need to install Java and Java3D first:



It may also be worth installing these on older versions of MacOS if you would like 
some small extra features. The new Java3D version you download will add 'shininess'
and 'pick highlighting' features.

Step 2: Drag-and-drop the MollyCule Application into your Applications 
folder. Please don't run MollyCule from the DMG file; you won't be able 
to save any data if you do that.

Step 3: Run MollyCule from the Applications folder like any other program.


Mollycule is supported on older versions of Windows such as Windows XP. 

Mollycule is not supported on the most recent versions of Windows 
such as Windows 7.

However, it should work on Windows 7 if you install it to a special
folder. Please read this page for more information:

General instructions for all Windows users:

Step 1: You MUST first install Java if it is not already installed, and 
secondly, you must install Java3D. These are two different downloads, 
and two seperate installations.

You can find each of them here:



You want to get the windows-i586-exe file from the Java3D website. 

Step 2: Download and right-click on it to extract the zip to your desktop. 
Please do not try to run MollyCule from 'inside the zip file' without extracting it. 
Be aware that 'double-clicking' the zip file will not extract the files; you must extract
 them with a right mouse click.

Step 3: Double click the MollyCule.jar file to run the program. If you 
encounter any problems, please report them to me - thanks!


Step 1: Install Java and Java3D if they are not already installed.

Step 2: Copy MollyCule to your hard disk e.g. ~/MollyCule

Step 3: Edit to have the correct PATH to Java. You may also need 
to add the directory for Java3D to the classpath, if it is not installed 
in your main Java folder. 

Step 4: Type ./ to run the program.