Presenting molecular models to colleagues, students, or during talks can often lead to a common issue: overwhelming your audience with too much structural detail all at once. When atoms and bonds appear simultaneously, even well-prepared presentations can become visually confusing, especially for those not deeply familiar with complex molecular topologies. Fortunately, SAMSON provides an elegant solution to this visualization challenge with its Reveal atoms animation effect.
The core idea behind the Reveal atoms animation is simple yet powerful: atoms (and the bonds between them) progressively appear in a controlled manner between two frames. This progressive appearance is achieved not through changing transparency, but by controlling the visibility of atomic nodes in the animation timeline. The result is a smoother, more understandable transition, particularly helpful when introducing unfamiliar structures or emphasizing assembly processes.
Why reveal atoms progressively?
Here are some common use cases where the Reveal atoms feature is worth considering:
- Educational explanations: Build up a molecule step-by-step to help students grasp connectivity and order.
- Presenting reaction mechanisms: Show intermediates forming over time for better conceptual flow.
- Storytelling with biomolecules: Introduce molecular domains one at a time to emphasize functional components before showing the complete structure.
How it works
To use the Reveal atoms animation, you simply:
- Select the atoms and bonds you’d like to progressively appear.
- Open the Animation panel in the Animator interface.
- Double-click on the Reveal atoms effect.
Understanding the animation timeline
The Reveal atoms animation introduces four keyframes:
- Keyframes 1-2: All selected atoms and bonds are hidden.
- Keyframes 2-3: The atoms and bonds begin to appear progressively based on the selection order.
- Keyframes 3-4: All selected atoms and bonds are now fully visible.
This gives you full control over when and how your molecular structure emerges. You can adjust the timing by moving keyframes on the timeline. For instance, slowing down the transition between keyframes 2 and 3 helps accentuate details, while shortening it creates a snappier effect.
Add nuance with easing curves
SAMSON also allows you to add expression using easing curves. These interpolate the visibility parameters so the animation can accelerate, decelerate, or follow more complex dynamics. This is useful when you want the reveal to feel more organic or direct the viewer’s attention.
Tips for better visibility control
- Grouped selections (e.g., residues or domains) can help manage what appears together.
- Use animation labeling so you can easily track effects applied to different atom groups.
- Preview the animation frequently and use the timeline scrubbing to control the pace in fine detail.
Whether you’re building a biomolecular presentation or an educational module, the Reveal atoms animation provides a cleaner, more pedagogical way to present your models, at your pace.
To learn more, visit the Reveal atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.