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Molecular graphics is the philosophy of studying molecules and their property through graphical representation. On a graphical display device, UPAC limits the definition to representations. There has been a history of hand-drawn molecules and atoms, ever since Dalton’s atoms and Kekule’s benzene, and these representations had an important influence on modern molecular graphics. This article concentrates on the use of computers for creating molecular graphics. Many molecular graphics systems and programs have close coupling between the editing commands, graphics or calculations such as in molecular modeling. From physical materials, there has been a long tradition of creating molecular models. Perhaps, the best known is Watson and Crick model of DNA built from planar sheets and rods. The most commonly used approach is to represent all bonds and atoms explicitly by using the “ball and stick” approach. This can validate a wide range of properties, such as relative size, shape, and flexibility. The goal of mainstream molecular graphics is to represent the “ball and stick” model as realistically as possible and to couple it with calculations of molecular properties. Computer models and physical models have partially complementary weaknesses and strengths. Without access to a computer, physical models can be used, and now can be made cheaply out of plastic materials. Their visual aspects and tactile cannot be easily reproduced by computers. The flexibility of molecules is also difficult to appreciate on a computer screen, illustrating the pseudorotation of cyclohexane is a good example of the value of mechanical models. It is difficult to build large physical molecules and all-atom physical models of even simple proteins, could take months or weeks to build. However, physical models are not robust, and they decay over time. Molecular graphics is particularly valuable for representing local properties of molecules and global, such as electrostatic potential. Graphics can also be animated to represent chemical reactions and molecular processes a feat which is not easy to reproduce physically. Both graphic arts and computer technology have contributed to molecular graphics. In the 1950s, the development of structural biology led to a requirement to display molecules with thousands of atoms. Most systems, therefore, used conventions in which information was stylistic implicit. Two vectors meeting at a point implied an atom or a complete residue.

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