TinkerCell now uses "Themes" to categorize graphics object. Each Theme is defined by a set of Nodes, Arrows, and Decorators. Each theme rests in a folder. There are three themes as of today:
Fancy1, Bio1, Blocks1
These themes are located inside the Graphics folder. In TinkerCell Options->"Select Theme" is used to switch between themes. TinkerCell searches the home folder (i.e. Documents/TinkerCell) first, which means that users can make new Themes and place them in the home folder.
Here is how to make a new Theme:
1. Create a folder in the Documents/TinkerCell folder called "Graphics"
2. Inside Graphics, create a folder with any name. The folder name is the name of your theme
3. Make three folders inside your theme folder: Nodes, Arrows, Decorators (case sensitive, I think)
4. Use the NodeGraphics program to make nodes, arrows, and decorators xml and PNG files, and put those files in the appropriate folders. Note that the NodeGraphics program creates an xml file (the vector graphics) and a PNG file (used to draw buttons).
5. Make sure that the names are correct. Eg. the .xml and .PNG file for drawing "Protein" types should be names Protein.xml, and the arrow for EnzymeCatalysis reactions should be names EnzymeCatalysis.xml. The Decorators should also use process family names, e.g. EnzymeCatalysis. You may want to look at the existing TinkerCell/Graphics folder.
6. Once you are done with your Theme, create a drawing in TinkerCell using your theme. Take a screenshot and save the "screenshot.png" file in your Theme folder. The Options->"Select Theme" dialog will display this file.