A molecular structure can contain far more detail than an audience needs to follow a presentation. Showing every atom throughout an explanation may make it difficult to focus on the region or components you are discussing. Concealing atoms progressively offers another option: guide attention by making selected atoms and the bonds between them disappear over time.
In SAMSON, the Conceal atoms animation works by changing node visibility, not transparency. That distinction matters: atoms are hidden rather than gradually becoming see-through. The animation is useful when you want a clean transition from a complete view of a selected group to a view in which that group is no longer displayed.
Build a transition around a selection
Start by choosing the atoms and bonds you want the animation to affect. Then double-click Conceal atoms in the Animation panel of the Animator. The animation is applied to the specified selection, so a useful first step is to decide what the audience should see before and after the transition.
For example, you might use the animation to move from a view that includes a selected set of atoms to one that gives the remaining structure more visual prominence. This is a presentation choice, not a change to the molecular structure itself: the animation controls whether the selected nodes are visible in the scene.
Understand the four keyframes
The animation has four keyframes, which divide the transition into three parts:
- Keyframes 1–2: the specified atoms and bonds are shown.
- Keyframes 2–3: the specified atoms progressively disappear. The animation hides atoms, along with bonds between hidden atoms, according to their order in the selection.
- Keyframes 3–4: all specified atoms and bonds are hidden.
This structure gives you more control than a single instant hide: the middle section creates the progressive change, while the first and last sections establish the fully shown and fully hidden states. If the transition feels too rushed or takes too long, move the keyframes to adjust when each part occurs. The keyframes can be moved whenever needed.
Use selection order deliberately
Because the progressive stage depends on the order of atoms in the selection, selection order is worth considering when planning the effect. Think about the sequence in which you want the structure to recede from view, and prepare the selection with that sequence in mind. The documentation does not prescribe one universal order: the right choice depends on what you want viewers to notice as the selected atoms disappear.
It also helps to preview the animation in the context of the full presentation. Ask whether the audience can still understand the structure at each point in the transition, and whether the final hidden state makes the next part of your explanation easier to follow. A progressive conceal can support a visual narrative, but the selection should have a clear purpose.
Adjust the feel of the transition
The Easing curve changes how parameters are interpolated between frames. If the timing or character of the transition does not fit your presentation, adjust the easing curve and move the keyframes as needed. These controls let you shape the animation without changing which atoms and bonds were selected.
Here is the documented example of the Conceal and Reveal atoms animations in action:
For a practical reference, the documentation also links to presentations that use this animation: 1AF6 – Fly around and 1AF6 – Fly around – 2.
To see the complete animation instructions, visit the Conceal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.