Make a Molecular Structure Unfold, One Selected Atom at a Time

A molecular model can be accurate and still be difficult to explain. When a whole structure appears at once, viewers may struggle to follow which atoms matter or how different parts relate. A progressive reveal offers a simple visual solution: start with the selected atoms hidden, then bring them into view in sequence.

In SAMSON, the Reveal atoms animation makes selected atoms—and bonds between them—appear progressively. It changes the visibility of nodes; it does not make them transparent. That distinction matters when planning a presentation: a hidden atom is not merely faint or see-through. It is not shown until the animation reveals it.

Build the reveal in four keyframes

Start by selecting the atoms and bonds you want the animation to affect. Then double-click Reveal atoms in the Animation panel of the Animator. The effect has four keyframes, giving the reveal a clear beginning, transition, and finish:

1. Keyframes 1 to 2: the specified atoms and bonds become hidden.
2. Keyframes 2 to 3: the selected atoms progressively appear. Bonds between atoms that have appeared are shown as well.
3. Keyframes 3 to 4: all the specified atoms and bonds are shown.

This structure is useful when you want a visual explanation to have a deliberate order rather than presenting every selected part at once. For example, you can use the animation to guide attention through a selected set of atoms, then leave the complete selection visible at the end. The animation does not determine a scientific narrative for you; the order comes from the selection.

Selection order is part of the presentation

During the transition from keyframe 2 to keyframe 3, atoms appear depending on their order in the selection. So if the reveal feels confusing, check the selection before changing the animation itself. Ask what sequence would be easiest for someone else to follow, and arrange the selected atoms accordingly. A carefully chosen order can make a dense model easier to inspect without changing the underlying structure.

It is also worth distinguishing the animated selection from the entire model. The documented behavior applies to the specified atoms and bonds. Before presenting, confirm that you selected the parts you intend to reveal and that the final keyframe shows the complete intended selection.

Adjust the pacing with keyframes

You can move the animation’s keyframes as needed. This lets you adjust when the hidden state begins, how much time is available for the progressive reveal, and when the full selection is visible. If viewers need time to follow the sequence, give the reveal more room; if the transition is only a brief cue, position the keyframes to suit that purpose.

You can also change how parameters are interpolated between frames by modifying the Easing curve. In practical terms, keyframe placement and easing are the controls to revisit when the transition does not feel right. The keyframes shape the timing, while the easing curve changes the interpolation between them.

A useful final check is to play through the animation from the beginning: make sure the selected parts are hidden before the reveal, appear in the intended selection order, and are all visible by the end. This helps catch a mismatch between the story you want to tell and the sequence the viewer sees.

For the complete instructions, see the Reveal atoms documentation.

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