The most classical wire model that uses wires to visualize the bonds and angles of the atoms. This model clearly shows the type of atoms in the molecule, the distances between bonds, and angles associated with the atoms. Because the lines drawn are very thin, molecules can very easily be manipulated when viewed on a computer screen. 

It is an extension of the wire model, in which the bonds are represented by cylinders. The position of the atoms remains the same, but are represented by the ends and branch points of the cylinder. This model clearly simply shows the whole molecule as a stick as opposed to a wireframe  It is visually easy to see, so it is used in various molecular modeling software. The color palette used is the same for most software for basic atoms such as red for oxygen and blue for nitrogen, but differences can be seen for other atoms.

In this model, atoms are depicted as color-coded balls or spheres, specific to different elements. The chemical bonds that connect the atoms are represented by rods similar to the stick model and are easier to visualize. In doing so, the sizes of the balls are made relatively smaller, thereby compromising on the proportional correlation with the actual atomic size. Yet, the ball-and-stick model defines the angles between atoms, clearly depicting the molecular geometry of simple to more complex structures as compared to other molecular models. In many cases, the type of atom is represented by the color of the sphere. As with the stick model, the bond angle and bond distance represent realistic values, but the size of the atom has no physical meaning.

Space-filling models are most realistic. They represent atoms as spheres that reflect the relative size of the atomic radius, where the atoms are scaled up in size to fill the space between each other. Since the spherical surface is determined based on the van der Waals radius of the atom, it is easy to intuitively grasp the size of the molecule and the positional relationship of the atoms. The size and position of an atom in this model are determined by its bonding properties and van der Waals radius, or contact distance. The van der Waals radius describes how closely two atoms can approach each other when a covalent bond does not link them. The spheres in this model illustrate the relative space occupied by each atom within a compound, while the angles  between atoms are not clearly visible.

Space-filling models are also referred to as CPK models after the chemists Robert Corey, Linus Pauling, and Walter Koltun,  

Here's an example: the stick and line models are cluttered and difficult to grasp the structure, while the manga model is dedicated to the secondary structure, making it easier to understand the structural features.