Make a molecular structure unfold, one selected atom at a time

A molecular model can be difficult to explain when the whole structure appears at once. Viewers may struggle to follow which part matters, especially in a presentation or animation intended to guide attention through a complex structure. A progressive reveal offers a simple alternative: show the selected atoms and their bonds in stages, so the structure builds on screen rather than arriving all at once.

In SAMSON, the Reveal atoms animation does this by changing node visibility—not by fading atoms through transparency. That distinction is useful when you want a clear, discrete reveal: atoms are hidden or shown, rather than appearing as ghosted, semi-transparent versions of themselves.

A four-keyframe reveal

The animation uses four keyframes to shape the sequence:

1. Keyframes 1–2: The selected atoms, along with bonds between them, become hidden.
2. Keyframes 2–3: They progressively appear. Which atoms are shown depends on their order in the selection, and bonds between shown atoms appear with them.
3. Keyframes 3–4: All selected atoms and the bonds between them are shown.

This structure gives the animation a beginning, a progressive middle, and a complete ending. It can help turn a static selection into a sequence that is easier to follow, without requiring the viewer to infer the order from a fully visible model.

A practical workflow

Start by selecting the atoms and bonds you want the animation to affect. Because the progressive stage follows the order of the selection, consider that order when planning how you want the reveal to read. For example, you might arrange the selection to follow the visual progression you want to communicate. The key point is to check the result in the animation: the order of appearance is tied to the selection, not an unrelated automatic storytelling rule.

Next, open the Animator, find Reveal atoms in the Animation panel, and double-click the effect to add it. Then play the animation and review the transition. If the reveal feels too fast, too slow, or poorly timed for your explanation, move the keyframes. They can be repositioned as needed, so you can adjust when the hiding, progressive reveal, and completed state occur.

Make the transition easier to read

Timing is only part of the effect. You can also modify the easing curve to change how the animation parameters are interpolated between frames. This gives you a way to adjust the character of the transition while keeping the same keyframe structure. After changing the curve or moving keyframes, review the animation again to make sure the reveal remains easy to follow.

One practical check is to watch the animation at the pace at which you expect to present it. Can someone identify the selected region as it appears? Does the completed structure remain visible long enough to understand? Adjusting keyframe positions and easing can help answer these questions without changing the molecular content itself.

Use Reveal atoms when you want a selected part of a model to build into view progressively. For other visibility effects, SAMSON also provides animations such as Conceal atoms, Appear, Disappear, Show, and Hide; the best choice depends on whether you need a progressive reveal or a different kind of visibility change.

Read the Reveal atoms documentation to learn more about adding and adjusting the animation.

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