A haem group has been made transparent. I think this looks damn fine. Above is a diagram of a wir plot. Alpha helices can be seen at H1 to H5. Red lines represent the anti-parallel beta sheets looping around themselves.
Purple arrows are beta strands.
The 2 diagrams below are of the molecule Phosphoenolpyruvate Carboxykinase from the organism E. Coli. The pink swirls in the above picture represent alpha helices, and the yellow strands represent b-pleated sheets. This diagram clearly shows the ligand component of the protein. Consisting of an ATP and OXL molecule, and a Magnesium atom displayed in green.