Relation To Molecular Models
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.
Read more about this topic: Molecular Graphics
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