Molecular graphics

Molecular graphics is both a field and a way of thinking about molecules by turning them into pictures. The International Union of Pure and Applied Chemistry (IUPAC) narrows this down to images shown on a "graphical display device." Long before computers, people drew atoms and molecules by hand—think of Dalton’s atoms or Kekulé’s benzene ring—and those early sketches still shape how we visualize molecules today. Colorful molecular graphics often appear on chemistry journal covers as art.

**History**

Before computer graphics came along, Robert Corey and Linus Pauling built physical models from hardwood, using a scale of 1 inch per angstrom and clamps to hold the structure together. These models introduced the CPK color scheme—carbon black, oxygen red, nitrogen blue, and so on—still used to tell atoms apart. In 1966, W.L. Koltun improved the design, creating what we now call Corey-Pauling-Koltun (CPK) models.

The first computer-based molecular models came from Project MAC in the mid-1960s, using wireframes on a cathode ray tube. In 1965, Carroll Johnson released the Oak Ridge thermal ellipsoid plot (ORTEP), which showed molecules as ball-and-stick figures with lines for bonds and ellipsoids for thermal motion. ORTEP quickly became the standard for X-ray crystallography and remains common today. The first practical use of molecular graphics was a wireframe display of the protein myoglobin in 1966, done by Cyrus Levinthal and Robert Langridge at Project MAC. A key advance in high-performance graphics came from Nelson Max, who created "realistic" renderings of macromolecules using reflective spheres.

In the 1970s, 3D display methods improved with cathode ray tubes and continuous-tone graphics paired with electro-optic shutter glasses. Early systems used active shutter 3D, sending different views to each eye for a stereoscopic effect. Those glasses relied on lead lanthanum zirconate titanate (PLZT) ceramics as shutters and needed batteries to sync with the display. Today, passive polarized 3D glasses are more common because they’re cheaper and let the wearer perceive depth naturally.

Macromolecular crystallography pushed molecular graphics forward because building physical models couldn’t keep up. The first two protein structures solved without the Richards’ Box were built using Stan Swanson’s program FIT on a Vector General display in Edgar Meyer’s lab at Texas A&M University. First, Marge Legg in Al Cotton’s lab solved a higher-resolution structure of staph. nuclease in 1975, then Jim Hogle solved monoclinic lysozyme in 1976. It took a full year before other graphics systems replaced the Richards’ Box for 3D density modeling. Alwyn Jones’ FRODO program (and later "O") let scientists overlay electron density from X-ray crystallography with hypothetical molecular structures.

**Types**

*Ball-and-stick models*: Atoms are small spheres, and rods connect them to show chemical bonds.

*Space-filling models*: Atoms are solid spheres sized by their van der Waals radii, overlapping where bonds form, to suggest the space they occupy.

*Surfaces*: Some models show a shaded surface that represents a physical property, like electronic charge density.

*Ribbon diagrams*: These schematic drawings of protein structure are now a standard way to depict proteins. A smooth curve traces the polypeptide backbone, showing the overall path and organization in 3D. α-helices look like coiled ribbons or thick tubes, β-strands appear as arrows, and loops or coils are lines or thin tubes. The chain’s direction is shown by the arrows, and a color ramp along the ribbon can indicate the sequence from start to end. Ribbon diagrams also provide a framework for adding atomic details, like oxygen atoms bound to myoglobin’s active site.