The atom is the smallest unit of matter that retains the properties of a greater whole. It is not indivisible, but pieces of atoms, especially the "chunks" of nuclear components called quarks, are really only good for making atoms. Different kinds of atoms are called elements, of which nearly 120 (92 of them naturally occurring) are known.

Most matter consists of multiple kinds of atoms, arranged in groups of two or more and having specific formulas; two or more atoms chemically bonded together make up a molecule. For example, a water molecule has the formula H₂O, meaning that it is made of the elements hydrogen (H) and oxygen (O) in a 2-to-1 atomic or molar ratio.

Calcium is a well-known element, being essential for good bone health and other functions in the human body. The calcium atom is neither a small nor an especially cumbersome atom, making it a good candidate for building a three-dimensional atom model project to illustrate the salient points of this structure.

Atoms consist of an equal number of protons and electrons in their basic (non-ionized) state, numbering from one to 118 as of 2020. The number of protons, the atomic number, defines the element. All elements except hydrogen also have one or more neutrons; protons and neutrons are about equal in mass (on the order of 10⁻²⁷kg), while electrons are almost 2,000 times smaller.

The number of protons and neutrons is roughly equal, although as you move upward through the periodic table of elements, neutrons begin to visibly outnumber protons in most atoms. Variants of elements that differ only in neutron number are called isotopes.

The negatively charged electrons occupy spaces far, far from the proton, at least on the scale of an atom, which is only about 1 × 10⁻¹⁰ m across. These are found in energy levels or shells, which for many atoms include subshells. Subshells in turn contain orbitals, each of which can hold up to two electrons.

Each row of the periodic table represents a shell, with the number of electrons a shell can hold being two, eight, eight and 18 in the first four rows of the periodic table.

You can see from the periodic table that calcium has an atomic number of 20 and an atomic mass of 40.78 daltons. This means that the most stable isotope of the element has 20 neutrons (40 − 20). You could pick green balls to represent protons and similarly sized orange balls to represent neutrons, and smaller yellow balls or marbles to represent electrons.

You can arrange your "protons" and "neutrons" into a ball-like nucleus, perhaps gluing them together, and then decide how to arrange your electrons.

From the table, you see that calcium has two electrons in the first shell (both in what's called the 1s subshell), eight in the second shell (2 in the 2s subshell, 6 in the 2p subshell), eight in the third shell (2 in the 3s subshell, 3 in the 3p subshell) and two in the fourth shell. These are calcium's valence, or chemically reactive electrons.

Consult different online references to see how electron subshells are depicted in 3D space. You could draw a calcium atom diagram to accompany your model, so as to cover any information you may find difficult to present visually.

A neon atom model could familiarize viewers with the concept of noble gases and full valence shells, for example, or a sodium atom model could serve as a representative simple metal that bonds to halogens such as chlorine.