Molecular+graphics

is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device".Ever since Dalton's atoms and Kekulé 's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. This article concentrates on the use of computers to create molecular graphics. Note, however, that many molecular graphics programs and systems have close coupling between the graphics and editing commands or calculations such as in molecular modelling.

There has been a long tradition of creating molecular models from physical materials. Perhaps the best known is Crick and Watson's model of DNA built from rods and planar sheets, but the most widely used approach is to represent all atoms and bonds explicitly using the "ball and stick" approach. This can demonstrate a wide range of properties, such as shape, relative size, and flexibility. Many chemistry courses expect that students will have access to ball and stick models. One goal of mainstream molecular graphics has been to represent the "ball and stick" model as realistically as possible and to couple this with calculations of molecular properties. //Figure 1// shows a small molecule (NH3CH2CH2C(OH)(PO3H)(PO3H)-), as drawn by the Jmol program. It is important to realize that the colors and shapes are purely a convention, as individual atoms are not colored, nor do they have hard surfaces. Bonds between atoms are also not rod-shaped. History: Initially the rendering was on early Cathode ray tube screens or through plotters drawing on paper. Molecular structures have always been an attractive choice for developing new computer graphics tools, since the input data are easy to create and the results are usually highly appealing. The first example of MG was a display of a protein molecule (Project MAC, 1966) by Cyrus Levinthal and Robert Langridge. Among the milestones in high-performance MG was the work of Nelson Max in "realistic" rendering of macromolecules using reflecting spheres. By about 1980 many laboratories both in academia and industry had recognized the power of the computer to analyse and predict the properties of molecules, especially in materials science and the pharmaceutical industry. The discipline was often called "molecular graphics" and in 1982 a group of academics and industrialists in the UK set up the Molecular Graphics Society (MGS). Initially much of the technology concentrated either on high-performance 3D graphics, including interactive rotation or 3D rendering of atoms as spheres (sometimes with radiosity). During the 1980s a number of programs for calculating molecular properties (such as molecular dynamics and quantum mechanics) became available and the term "molecular graphics" often included these. As a result the MGS has now changed its name to the Molecular Graphics and Modelling Society (MGMS). The requirements of macromolecular crystallography also drove MG because the traditional techniques of physical model-building could not scale. Alwyn Jones' FRODO program (and later "O") were developed to overlay the molecular electron density determined from X-ray crystallography and the hypothetical molecular structure.