Pauling’s Rules grew from an understanding of chemistry and physics, but also involved a new passion of Pauling’s: model building. His interest in the structure of molecules led naturally to an approach based on the visualization of those structures. Pauling thought of molecules in three dimensions. While in Germany he had seen some elegant models of molecules made of wooden balls and wires, and he brought home an understanding of the value of accurate model-building.

In his attack on complex crystal structures, Pauling combined his Rules with model-building. He knew for example that oxygen atoms in crystals often formed an octahedron, a cube-shaped arrangement, with other elements. Carbon formed tetrahedra. Sodium and chlorine took a cube-shaped arrangements in table salt. With these basic building-block shapes in mind, Pauling used his Rules to determine how they fit together, whether they shared a side or a face or a point. He began doodling pictures and then, with Ava Helen’s help, started folding three-dimensional shapes out of paper and sewing them together. These paper models helped him tremendously: He could now see what fit and what did not, and could try new combinations again and again.

The models were made painstakingly, using what was known about the sizes of atoms and ions, fitting what was known about bond lengths and angles from x-ray crystallography studies, matching the dictates of Pauling’s Rules.

When he created a model that seemed to fit all the data, he could work backwards, judging what sort of complex x-ray pattern his model might create instead of using the x-ray pattern to determine the structure.

In later years, Pauling frequently collaborated with a talented artist named Roger Hayward to illustrate Pauling's ideas on the shapes and orientations of atoms and molecules.