When building animations in molecular modeling, a common challenge is highlighting which atoms or residues are appearing, disappearing, or changing over time. For presentations, educational videos, or simple visualization clarity, we often need a way to guide the viewer’s focus step by step—especially as large molecular systems can quickly feel overwhelming.
One subtle but effective feature in SAMSON is the Reveal atoms animation. Rather than adjusting transparency or color, it offers a progressive visibility-based way to make atoms and their corresponding bonds appear gradually in a scene. This neat effect can be very useful when showing molecular assembly processes, secrets within protein pockets, or stepwise molecular interactions 🧬.
What’s different about Reveal atoms?
Unlike animations that toggle opacity or color fluctuation, Reveal atoms works by precisely hiding and then showing atoms based on keyframes. This doesn’t involve visual tricks based on transparency; the atoms are either in the viewport or not—giving complete control over what your audience sees at each moment.
Here’s how this animation breaks down over four keyframes:
- Keyframes 1 → 2: All chosen atoms and bonds are hidden;
- Keyframes 2 → 3: Atoms reappear progressively, based on the order in which you selected them;
- Keyframes 3 → 4: All atoms and bonds are fully shown.
This technique is particularly helpful if you’re working with assembly models or illustrating how a ligand binds within a receptor. The controlled reveal mimics a narrative flow—one atom at a time—something viewers can follow intuitively.
How to use it efficiently
1. First, select the atoms and bonds you want to appear progressively. The order of selection matters because it determines the reveal order.
2. Then, head to the Animation panel inside the Animator.
3. Double-click on the Reveal atoms animation. It will initialize four keyframes for your selection.
4. Adjust the placement of the keyframes along the timeline depending on how quickly or slowly you’d like the atoms to reveal.
Useful tip: customize the motion feel
If you want to adjust the speed or feel of the transition (linear, ease-in, ease-out), you can do that by editing the Easing curve. This setting allows you to fine-tune the behavior of the reveal: should it start slowly and then speed up? Or maybe the reverse?
Example in action
For instance, imagine you’re reconstructing a molecular structure from fragments. Assign the fragments in your preferred order, and let the Reveal atoms animation build the final structure atom-by-atom. This technique can even be combined with Conceal atoms to reverse the effect, allowing atoms to disappear gracefully.
Feel free to re-arrange your keyframes anytime. This flexibility means you’re never locked into one story: you can refine how structures appear as your scientific narrative evolves.
Learn more about this animation at 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.