A molecular structure can be difficult to present when the audience needs to focus on one region, but the surrounding atoms keep competing for attention. Hiding everything at once can make the transition feel abrupt; fading atoms with transparency can also leave a confusing image of overlapping, partly visible bonds. A more deliberate approach is to make selected atoms and their bonds disappear progressively.
In SAMSON, the Conceal atoms animation does this by changing node visibility—not transparency. That distinction matters: as the animation progresses, atoms and the bonds between them are hidden, rather than left faintly visible. This can help you guide attention through a structure while keeping the visible part clear.
Build a transition around the question you want to answer
Before adding the effect, decide what the viewer should notice first and what can disappear from view. For example, you might want to introduce a selected set of atoms in full, then progressively conceal them, and finally leave them hidden so the next part of the structure can take visual priority. The animation is not a substitute for choosing a useful selection: it operates on the atoms and bonds you specify.
Set up the animation
- Select the atoms and bonds you want to conceal. The animation affects the specified atoms and the bonds between them.
- Add the effect. In the Animator’s Animation panel, double-click Conceal atoms.
- Check the four keyframes. Between keyframes 1 and 2, the specified atoms and bonds are shown. Between keyframes 2 and 3, they progressively disappear. Between keyframes 3 and 4, they are hidden.
- Move the keyframes to adjust when the stages occur in your presentation.
The middle part of the animation is especially useful to review. Atoms and bonds disappear according to their order in the selection. That means the sequence is not necessarily a spatial sweep across the molecule; it depends on the selection order. If the progression looks unexpected, revisit the selection and preview the animation before presenting it.
Use timing to make the change legible
A progressive concealment can help viewers follow a change that would be easy to miss if the whole selection vanished at once. Give the transition enough time for the audience to understand what is being removed, then place the final hidden state where it supports the next moment in your explanation. You can move the animation’s keyframes to change its timing. You can also modify the easing curve to change how parameters are interpolated between frames.
Keep the purpose of the transition simple: clarify what should remain visible. Concealment is useful when you want selected atoms and their connecting bonds to leave the view, not when you need them to remain visible as a transparent layer. If you want the reverse progression, SAMSON’s animation documentation also lists Reveal atoms.
For the animation’s full setup details and examples, learn more in the Conceal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.