When working with molecular systems, storytelling isn’t just helpful—it’s essential. Whether you’re trying to communicate a complex biochemical process or guide someone through your model step by step, the way you present atoms and interactions makes all the difference. One common challenge molecular modelers face is: how can I show atoms progressively to help viewers intuitively understand the structure or process?
The Reveal atoms animation in SAMSON provides one way to do just that. Rather than fading atoms in or setting their transparency, this animation controls their visibility frame by frame, helping you build anticipation, guide attention, or highlight changes with precision.
Why progressive atom appearance matters
Let’s say you want to depict ligand binding, show how a mutation affects a pocket, or simply focus attention on a specific region of a macromolecule. If you reveal the entire structure at once, that can be overwhelming. But by using a controlled reveal, you can:
- Highlight critical regions gradually
- Show step-by-step assembly or interaction sequences
- Create cleaner and more engaging animations
The basics of the Reveal atoms animation
To use this animation, simply choose the atoms (and the bonds between them) you want to reveal, then double-click Reveal atoms in the Animation panel of the Animator.
The animation consists of four keyframes:
- Frames 1–2: All selected atoms and bonds are hidden.
- Frames 2–3: Atoms and bonds progressively appear in selection order.
- Frames 3–4: All selected atoms and bonds are fully visible.
The order in which atoms appear depends on the selection order, so taking a moment to select atoms intelligently can improve the storytelling aspect of your animation.
Fine-tuning the pace
You can adjust when these atoms appear by moving the animation’s keyframes along the timeline. This means you can decide exactly when the reveal begins and ends, syncing it with other events or narrative elements in your presentation. Additionally, the Easing curve setting allows you to smooth out or modify the pace of appearance, making for more natural motion.
Seeing it in action
Here’s an illustration of both the Conceal atoms and Reveal atoms animations used together:
In practice, these animations can be used for dynamic visualizations of ligand binding, disassembly of molecules, morphing between states, and more. Because visibility is controlled directly, there’s no ambiguity compared to transparent overlays.
A tip for smoother workflows
Remember that you can revisit and move your animation keyframes anytime. This makes it easy to try different timings and revise your sequences as your presentation evolves. Don’t hesitate to experiment with selection order, easing curves, and animation length—small adjustments can make the animation flow much more intuitively for your viewers.
To learn more about the Reveal atoms animation in SAMSON, check the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.