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 ----

MAC USERS

Step 1: Java and Java3D are already installed in Macos X. You don't need 
to do anything here. However, if you would like some small extra program 
features, you can install the latest Java3D (1.5) to make them 
available. This 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.



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.

The current version of Java is 1.6, and the current Java3D is 1.5.1.

You can find each of them here:

JAVA: http://www.java.com/getjava/ 

JAVA3D: https://java3d.dev.java.net/binary-builds.html

You want to get the windows-i586-exe file from the Java3D website. e.g. 
this one: 
http://download.java.net/media/java3d/builds/release/1.5.2/j3d-1_5_2-windows-i586.exe


Step 2: Copy MollyCule to your hard disk, perhaps the C: drive. 

Step 3: Next, you might need to edit Mollycule.sh or MollyCul.bat to 
make sure the PATH variable is set correctly. This line of the file must 
point to the place where "java.exe" is found. Usually this will be 
something like C:\Program Files\Java\jre6\bin...

Please set the PATH correctly for your computer (look inside "Program 
Files" on the C drive), or this java program cannot run. I've tried to 
guess where your 'java' will be stored on your computer, but you may 
need to set it yourself.

Step 4: Double click the MollyCul.bat file and the program will run! If 
nothing happens, the reason is because you haven't installed Java and 
Java3D, or you haven't set the PATH variable correctly in the .bat file.


LINUX USERS:

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 MollyCule.sh 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 ./MollyCule.sh to run the program.