To keep file sizes to a minimum, the VRML are not commented, but several have a seperate page explaining the nodes used ion the scene. You could represent the nucleus by a small solid sphere, and if necisary, use a second semi-transparent sphere to represent the electron cloud around it. Electron Orbitals Electron orbitals are also relatively simple. This can be approximated by the use of a very squashed sphere. The only slight complication is that angles of 109 degrees for example have to be used, instead of just 90 and 45 degrees.
Pi bonds are harder to represent than signma bonds for obvious reasons.
One way to show a pi bond is to show the two p orbitals, and then to build a semi-transparent cylinder between them. The p orbitals can be constructed in exactly the same way as they are in exaples 4 and 5. Large Molecules Larger molecules present many problems, the main one being their complexity. Creating a VRML file manually for something like Asparin would take a huge amount of time and patience, and even this is a relatively small and simple molecule. In order to create VRML files for large molecules, you would really need to use a software tool which did most of the work for you.