Molecules are stable collections of atomic nuclei with electrons swarming around them. A realistic representation could be possible, however, it would both be hard to create and even harder to understand. For this reason, simplified models are used, indicating the position of atoms (or more accurately their cores) and indicating bonds similar to a 2D skeletal formula. However, the possibility of visualizing the electrons of a molecule exist.

The element of an atom is usually indicated by color, sometimes supported by size. Different color schemes exist, with the most commonly used being the CPK coloring. Here at Chemistry in 3D we are using a custom scheme based on CPK coloring that is optimized for digital models. The most common atom colors can be seen here. If other elements are used the color is explained at that time.