A molecular structure can be difficult to explain all at once. When every atom and bond is visible from the beginning, viewers may struggle to follow which part they should focus on. A progressive reveal offers a simple alternative: start with the selected components hidden, then bring them into view in sequence.
In SAMSON, the Reveal atoms animation changes the visibility of atoms and bonds; it does not fade them in by adjusting transparency. That distinction matters when you want a clear, discrete build-up of a structure rather than a translucent-to-opaque effect. The animation can help make a presentation easier to follow by separating the moment when a component is introduced from the moment when it is simply present on screen.
How the reveal is staged
The animation uses four keyframes, which divide the effect into three stages:
- Keyframes 1–2: the specified atoms and bonds are hidden.
- Keyframes 2–3: atoms progressively appear. Which atoms appear along the way depends on their order in the selection; bonds between atoms that have appeared are shown as well.
- Keyframes 3–4: all specified atoms and bonds are visible.
This structure is useful for planning a visual explanation. The first interval establishes the hidden starting state, the middle interval carries the progressive reveal, and the final interval ensures the selected components are all shown. If the reveal feels rushed or lasts too long, you can move the animation’s keyframes to adjust its timing.
Prepare the selection before you animate
Choose the atoms and bonds you want the effect to act on, then add Reveal atoms by double-clicking it in the Animation panel of the Animator. Because the progressive stage depends on the order of atoms in the selection, selection order is not just a behind-the-scenes detail: it can affect the sequence viewers see. Before presenting the animation, preview it and check that the reveal progresses in a way that supports your explanation.
A useful planning question is: What should the viewer notice first, and what should become visible next? Use the selected set and its order with that viewing sequence in mind. For example, if your purpose is to introduce a structure in stages, consider whether the sequence reads naturally from the first visible atoms to the last. The documentation does not prescribe a particular molecular storytelling order; the right sequence depends on what you want to explain.
Adjust the pace, then refine the feel
Keyframe placement controls where the stages fall in the animation. Moving the keyframes gives you a way to allocate more or less time to the hidden, progressive, and fully visible portions. Once the timing is in place, you can modify the Easing curve to change how parameters are interpolated between frames. Easing affects the interpolation, while the selection order determines the sequence in which atoms appear; these are separate parts of shaping the result.
As a final check, watch the animation from its beginning through the fully visible state. Confirm that the selected atoms and bonds start hidden, that the intermediate sequence is understandable, and that the complete selection is visible at the end. This small review can catch confusing pacing or an unexpected reveal order before you use the animation to communicate your model.
For the exact setup details, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.