Make a molecular structure easier to follow, one group of atoms at a time

A dense molecular structure can be difficult to explain all at once. Important atoms may be buried inside a larger model, and simply pointing to them in a static view can leave an audience unsure where to look. A progressive reveal offers another approach: keep the structure in view, but introduce selected atoms and their connecting bonds in stages.

In SAMSON, the Reveal atoms animation changes the visibility of nodes. It does not make atoms transparent or fade them in. That distinction matters: this is a way to control which parts of the structure are visible, not a visual claim that the atoms are forming, moving, or changing chemically.

Build a reveal around the point you want to make

Start by selecting the atoms and bonds you want the animation to reveal. The selection defines what the effect acts on, so it is worth deciding what your audience needs to notice before adding the animation. For example, you might reveal a selected region after first showing the rest of the context, or use the sequence to guide attention through a larger model.

Then, in the Animator’s Animation panel, double-click Reveal atoms. The effect has four keyframes, which create three distinct stages:

1. Keyframes 1–2: the specified atoms and bonds are hidden.
2. Keyframes 2–3: they progressively become visible. The order of the selection determines the order in which atoms appear; bonds between atoms are shown as the relevant atoms become visible.
3. Keyframes 3–4: all specified atoms and bonds are shown.

This structure gives you a useful pause before the reveal, a progressive middle section, and a clear fully revealed endpoint. Consider what each stage should communicate: the initial view establishes context, the sequence directs attention, and the final view lets viewers inspect the complete selected region.

Selection order is part of the story

Because the reveal follows the order of the selection, that order affects what viewers see first. If the sequence seems confusing, review the selection rather than assuming the animation is showing atoms in a chemically meaningful or automatic order. Plan the sequence to support your explanation, and check the result in the actual animation before presenting it.

It can help to keep the selected region focused. Revealing a smaller, relevant group is often easier to follow than introducing many unrelated parts at once. If your explanation has several stages, consider whether separate reveals would make the visual sequence clearer than one long reveal. The animation controls visibility; it does not add labels or explain the significance of the atoms, so your narration or accompanying material should supply that context.

Adjust timing without changing the selection

You can move the animation’s keyframes to change when each stage occurs. Give the audience enough time to register the initial context and the completed structure, and adjust the interval for the progressive reveal to suit the pace of your explanation. There is no single timing that fits every structure or presentation.

You can also change how parameters are interpolated between frames using the easing curve. This affects the interpolation between keyframes, while the reveal’s key stages remain the same. Preview the animation after moving keyframes or changing easing so you can confirm that the visual pacing still supports your point.

Use this effect when the challenge is not merely showing a structure, but helping someone follow which part matters. A deliberate selection, a sensible order, and well-placed keyframes can turn a crowded view into a more understandable visual explanation—without suggesting that visibility changes are molecular motion.

Learn more about the Reveal atoms animation in the SAMSON documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.