One common challenge in molecular modeling and presentations is how to communicate structural changes without losing clarity. Whether you’re showing molecular growth, selective syntheses, or conformational changes, visualizing atoms appearing gradually—not all at once—can be much more effective.
This is where the Reveal atoms animation in SAMSON comes into play.
Why progressive atom reveal matters
When you’re teaching, publishing, or even reviewing dynamic molecular simulations, a smooth and gradual transition allows viewers to follow the logic of a change step-by-step. Abrupt changes can be visually confusing, especially in dense systems.
Instead of relying on transparency or fading tricks, the Reveal atoms animation uses visibility. This means atoms—and bonds between them—simply appear progressively between two keyframes.
How it works
The process is built around four keyframes:
- Keyframe 1 to 2: selected atoms (and their bonds) are hidden.
- Keyframe 2 to 3: atoms begin to appear one by one, based on their order in the selection.
- Keyframe 3 to 4: all selected atoms and bonds are now fully visible.
This structure gives you fine control over exactly when and how the reveal happens. You could, for example, synchronize the appearance with a corresponding change in electronic configuration or demonstrate reaction intermediates becoming visible.
Customizing the transition
You’re not locked into a rigid timing. All keyframes are movable, and more advanced users can adjust the Easing curve to fine-tune the way atoms appear—whether linearly, with acceleration, or deceleration.
When to use this
This animation adds clarity in multiple scenarios:
- Visualizing molecular assembly: Gradually show structures building up atom by atom.
- Explaining mechanisms: Emphasize specific changes over time during a reaction.
- Creating educational materials: Help students see which atoms are added or emphasized.
- Comparative analysis: Show how a ligand or molecule changes over time or by condition.
To apply it, just select the atoms and bonds you’d like to animate and then double-click on Reveal atoms in the Animation panel of the Animator.
What it looks like
This animation example shows a combination of conceal and reveal effects used together for even greater visual clarity:
Want to see how this technique fits into your workflow? Learn more in the official documentation →
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.