When a molecular structure appears all at once, it can be difficult for viewers to follow what they should notice first. A progressive reveal can make the sequence easier to read—but only if the order and timing support the story you want to tell.
In SAMSON, the Reveal atoms animation makes selected atoms and bonds appear progressively between frames. It works by changing node visibility, not transparency. That distinction matters: this effect reveals or hides the selected nodes rather than gradually making them more transparent.
Plan the reveal before setting the timing
The key practical detail is that atoms are revealed according to their order in the selection. So, before adding the animation, think about the sequence you want an audience to follow. For example, you might organize a selection so that the parts you want viewers to notice first appear earlier than the rest. The animation follows that selection order; it does not independently decide which atoms are most important.
This is especially useful when a structure contains many atoms and bonds. A deliberate order can turn a dense view into a sequence of smaller visual steps. If the reveal feels confusing, review the selection order as well as the animation timing.
What the four keyframes do
Reveal atoms uses four keyframes, and each interval has a distinct role:
- Keyframes 1–2: the specified atoms and bonds are hidden.
- Keyframes 2–3: the selected atoms appear progressively in selection order. Bonds between atoms that have appeared are shown as well.
- Keyframes 3–4: all specified atoms and bonds are shown.
These stages give you a useful way to think about pacing. The first interval establishes the hidden starting state, the middle interval carries the progressive reveal, and the final interval completes it. You can move the keyframes to adjust where these stages fall in the animation. If viewers need more time to follow the sequence, consider giving the progressive interval more room; if the reveal should feel brisk, adjust the timing accordingly.
A simple workflow
- Select the atoms and bonds you want the animation to affect.
- Check that the selection order matches the reveal sequence you have in mind.
- In the Animator’s Animation panel, double-click Reveal atoms to add the effect.
- Move the keyframes as needed to set the timing of the hidden, progressive, and fully shown stages.
- Adjust the easing curve if you want to change how the animation parameters are interpolated between frames.
The easing curve changes interpolation between frames, while moving keyframes changes when the stages occur. Keeping those controls distinct can help when refining an animation: use keyframe placement to shape the timing, and the easing curve to adjust the transition between frames.
One detail to keep in mind
Reveal atoms is a visibility-based effect. If your goal is for atoms to fade gradually through transparency, this animation is not described as doing that. It is intended to progressively show selected nodes. Choosing the effect that matches the visual change you need can save time when building a molecular presentation.
For the full description, see the Reveal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.