More than a century after Ernest Rutherford discovered the positively charged particle at the heart of every atom, physicists are still struggling to fully understand the proton.

High school physics teachers describe them as featureless balls with one unit each of positive electric charge — the perfect foils for the negatively charged electrons that buzz around them. College students learn that the ball is actually a bundle of three elementary particles called quarks. But decades of research have revealed a deeper truth, one that’s too bizarre to fully capture with words or images.

“This is the most complicated thing that you could possibly imagine,” said Mike Williams, a physicist at the Massachusetts Institute of Technology. “In fact, you can’t even imagine how complicated it is.”

The proton is a quantum mechanical object that exists as a haze of probabilities until an experiment forces it to take a concrete form. And its forms differ drastically depending on how researchers set up their experiment. Connecting the particle’s many faces has been the work of generations. “We’re kind of just starting to understand this system in a complete way,” said Richard Milner, a nuclear physicist at MIT.

As the pursuit continues, the proton’s secrets keep tumbling out. Most recently, a monumental data analysis published in August found that the proton contains traces of particles called charm quarks that are heavier than the proton itself.

The proton “has been humbling to humans,” Williams said. “Every time you think you kind of have a handle on it, it throws you some curveballs.”

Recently, Milner, together with Rolf Ent at Jefferson Lab, MIT filmmakers Chris Boebel and Joe McMaster, and animator James LaPlante, set out to transform a set of arcane plots that compile the results of hundreds of experiments into a series of animations of the shape-shifting proton. We’ve incorporated their animations into our own attempt to unveil its secrets.

Proof that the proton contains multitudes came from the Stanford Linear Accelerator Center (SLAC) in 1967. In earlier experiments, researchers had pelted it with electrons and watched them ricochet off like billiard balls. But SLAC could hurl electrons more forcefully, and researchers saw that they bounced back differently. The electrons were hitting the proton hard enough to shatter it — a process called deep inelastic scattering — and were rebounding from point-like shards of the proton called quarks. “That was the first evidence that quarks actually exist,” said Xiaochao Zheng, a physicist at the University of Virginia.

After SLAC’s discovery, which won the Nobel Prize in Physics in 1990, scrutiny of the proton intensified. Physicists have carried out hundreds of scattering experiments to date. They infer various aspects of the object’s interior by adjusting how forcefully they bombard it and by choosing which scattered particles they collect in the aftermath.