A molecular model can contain exactly the detail you need for analysis and still be difficult to explain. When many atoms and bonds compete for attention, viewers may struggle to follow the part of the structure you want to discuss. Removing that detail all at once can be just as confusing: the audience loses the visual context that helps them understand what changed.
The Conceal atoms animation offers a more gradual approach. It progressively hides selected atoms—and bonds between them—across an animation. Rather than changing transparency, it changes node visibility. That distinction matters: the atoms do not fade into faint shapes; they become hidden as the animation progresses.
Use the transition to guide attention
Conceal atoms is useful when you want to move from a complete molecular view toward a less crowded one. For example, you might begin by showing the selected atoms and then let them disappear progressively, so viewers can follow the reduction in detail instead of having to interpret an abrupt change. This can help make a presentation easier to track, especially when the order in which atoms disappear is meaningful to the explanation.
The animation has four keyframes, arranged into three stages:
- Keyframes 1–2: the specified atoms and bonds are shown.
- Keyframes 2–3: the specified atoms progressively disappear. Which atoms are hidden depends on their order in the selection; bonds between hidden atoms are hidden as well.
- Keyframes 3–4: all specified atoms and bonds are hidden.
In practice, this means the selection is not merely a way to identify what the animation affects: its order can shape the reveal of the transition. Before presenting, consider what you want viewers to notice first, then check the selection order and preview the result. If the disappearing sequence does not support your explanation, adjust the selection or move the keyframes to give the transition a more useful pace.
A simple planning workflow
- Start with the story. Decide what should remain visible and what you want to remove from view. Conceal atoms affects the atoms and bonds you specify, so choose the intended set before adding the effect.
- Think about sequence. Because progressive hiding depends on selection order, review the order with the intended viewing experience in mind. Do not assume the transition is just a uniform fade of the whole selection.
- Place the animation. Choose the atoms and bonds, then double-click Conceal atoms in the Animation panel of the Animator.
- Set the timing. Move the keyframes as needed. A longer interval for the progressive stage gives viewers more time to follow which parts disappear; a shorter interval makes the change quicker. The exact timing should suit the point you are making.
- Check the complete sequence. Confirm that the selected atoms begin visible, disappear during the middle stage, and are hidden by the end. Previewing helps catch an unexpected order or a transition that moves too quickly for the audience.
You can also change how parameters are interpolated between frames using the easing curve. This gives you a way to adjust the character of the transition without changing the basic purpose of the animation: progressively hiding the specified atoms and bonds.
A useful rule of thumb is to treat concealment as a visual editing choice, not as a substitute for explaining what the viewer is seeing. The animation can reduce clutter and direct attention, but a clear sequence still depends on selecting the right atoms, ordering them intentionally, and giving the transition enough time.
For the full instructions, see the Conceal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.