A crowded molecular structure can be difficult to explain all at once. When every atom and bond is visible from the first frame, viewers may struggle to follow which part matters or how a model is being introduced. A progressive reveal can make a presentation easier to follow by showing a chosen set of atoms and bonds in stages.
In SAMSON, the Reveal atoms animation does this by changing node visibility—not by fading atoms in through transparency. That distinction matters: the atoms are hidden, then shown, rather than gradually becoming more opaque. The result is a sequence of visible additions that can help guide attention through a structure.
Plan the reveal around the story
Before adding the effect, decide which atoms and bonds you want the animation to reveal. Think about the order in which someone should inspect them. For example, you might want a viewer to notice one region before another, or to see a selected subset build up into a more complete view. The animation follows the order of items in the selection, so that order is part of the visual explanation—not just a technical detail.
Once you have selected the atoms and bonds, double-click Reveal atoms in the Animation panel of the Animator. The effect contains four keyframes, which divide the action into three useful phases:
- Keyframes 1–2: the specified atoms and bonds are hidden.
- Keyframes 2–3: atoms and bonds progressively appear. The sequence depends on their order in the selection.
- Keyframes 3–4: all specified atoms and bonds are shown.
This structure gives the animation a clear beginning, reveal, and completed state. It also helps avoid a common presentation problem: starting with the entire selected region already visible, then trying to explain its parts without a visual cue for where to look.
Use the timeline to control pacing
After adding the animation, move its keyframes as needed. Their placement on the timeline determines how much time is available for each phase. If the progressive reveal passes too quickly for a viewer to follow, adjust the keyframe spacing to give that section more time. If the animation feels slow, bring the relevant keyframes closer together. You can reposition keyframes, so you can refine the pacing without changing which atoms and bonds are included.
You can also change how parameters are interpolated between frames by modifying the easing curve. This affects the transition’s timing character. Consider the intended use: a narrated explanation may benefit from a pace that leaves room for commentary, while a brief overview may call for a shorter sequence. Preview the animation and check that the reveal order supports the explanation rather than competing with it.
A useful final check is to watch the animation without narration. Can you tell what is being introduced, and does the order make sense? If not, revisit the selection order or the keyframe timing. A deliberate reveal can make a complex view easier to read without changing the molecular model itself.
For the full instructions, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.