In molecular modeling and education, revealing just the right amount of detail at the right moment is crucial. Whether you’re preparing a presentation or building an instructional animation, visual clarity can make or break how well a concept is understood.
One common challenge is: how can you gradually hide specific atoms or regions of a molecule to guide the viewer’s attention throughout an animation? Rather than making everything vanish at once or using transparency (which may still leave visual clutter), a cleaner solution is to conceal atoms step by step.
This is exactly what the Conceal Atoms animation effect in SAMSON offers. It enables modelers to reduce visual complexity by progressively hiding selected atoms and the bonds between them. This method can be useful in a variety of situations:
- Showing the sequential disappearance of a ligand from a binding site
- Focusing attention on a functional group by concealing surrounding atoms
- Illustrating the movement or modification of substructures within a molecule
How it works
Once you have selected the atoms and bonds you want to include in the concealment, simply double-click the Conceal Atoms effect from the Animation panel in the Animator. The animation creates four keyframes:
- 1 to 2: all selected atoms and their bonds are fully visible
- 2 to 3: atoms and bonds are gradually hidden in a user-defined order
- 3 to 4: all selected atoms and bonds are completely hidden
Visibility is toggled based on the order of selection, not by modifying transparency. This leads to clear visual transitions and reduces unnecessary visual distraction.
A simple example
In the example below, you can see how atoms are progressively concealed to uncover the internal structure of a molecular system. It’s a clean, intuitive way to communicate molecular changes without overwhelming the viewer:
Refining with easing curves
The Conceal Atoms effect supports different easing curves that control the speed of the animation between keyframes. Want atoms to vanish with a smooth deceleration? Adjust the easing curve accordingly to produce a more natural motion feel.
Try it with real examples
To see how other molecular modelers have implemented this feature, explore these sample animations created with SAMSON:
This technique, although simple, empowers clear and focused molecular storytelling—from dynamic presentations to educational content.
To learn more and access the full documentation, visit the official page for the Conceal Atoms animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.