A molecular model can contain more detail than an audience can absorb at once. When you need to explain a binding site, a structural region, or the relationship between selected atoms, leaving every part visible can make the important features harder to follow. Hiding everything immediately creates the opposite problem: the audience may not see what changed.
The Conceal atoms animation offers a middle ground. It progressively hides selected atoms and the bonds between hidden atoms, making it possible to guide attention through a structure over time. The key detail is that this effect changes visibility, not transparency. Atoms do not become see-through; they disappear from view.
Build the explanation around the selection
Start by choosing the atoms and bonds you want to conceal. Then, in SAMSON’s Animator, double-click Conceal atoms in the Animation panel to add the effect. Because the animation operates on the selection, that choice defines what the audience will see change. A focused selection can help keep the visual story clear; a broad selection can be useful when you want a larger part of the model to leave the scene.
The animation has four keyframes, which divide the effect into three stages:
- Keyframes 1–2: The specified atoms and bonds are shown.
- Keyframes 2–3: They progressively disappear. Which atoms and bonds hide, and in what order, depends on their order in the selection.
- Keyframes 3–4: All specified atoms and bonds are hidden.
This staged behavior is useful when a sudden change would be difficult to interpret. For example, you can let viewers first see the selected region, then watch it recede, and finally examine the model with that region out of sight. The animation itself does not decide what the audience should notice; the selection and timing are what shape that explanation.
Use timing to control the pace
After adding the animation, move its keyframes as needed. Their positions determine how the stages fit into your presentation, so you can give the progressive concealment more or less time. If the change feels too abrupt or too gradual, you can also modify the easing curve, which controls how parameters are interpolated between frames.
One practical check is to preview the transition and ask two questions: does the audience have enough time to register what is disappearing, and does the order of disappearance support the point you are making? Since the selection order affects the progressive stage, it is worth checking that stage rather than judging the animation only from its beginning and end.
Visibility, not a fade
Choose Conceal atoms when the intended result is that selected atoms and their associated bonds leave view progressively. If you expected a transparency fade, this animation is not doing that: the documentation specifies that it works through node visibility rather than transparency. Understanding this distinction helps set expectations and makes it easier to choose an animation that matches the visual explanation you have in mind.
Conceal atoms is one of several related animation effects, including Reveal atoms, Appear, and Disappear. For the full setup details and examples, see the Conceal atoms documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.