In molecular modeling, clarity isn’t just helpful — it’s essential. Whether you’re preparing a research presentation, an educational video, or a visual abstract, making complex molecular systems understandable often means turning overwhelming detail into digestible focus.
One effective way to accomplish that in SAMSON, the integrative molecular design platform, is through the Conceal atoms animation. This animation lets you progressively hide specific atoms and bonds over time, helping spotlight the regions or mechanisms you want your audience to focus on.
Why hide atoms?
Imagine you’re visualizing a protein–ligand interaction. If the entire protein remains visible at all times, the binding site or conformational change you’re trying to demonstrate might get lost in the visual noise. Concealing atoms gives you the visual control to guide your viewer’s attention, by making secondary elements fade out as the animation progresses.
What does the animation actually do?
The Conceal atoms animation operates between 4 keyframes:
- Keyframes 1 → 2: All selected atoms and bonds are shown.
- Keyframes 2 → 3: Selected atoms and bonds progressively disappear, based on their order of selection.
- Keyframes 3 → 4: All selected atoms and bonds are fully hidden.
This isn’t just a change in transparency. The atoms are actually hidden from the scene — which means they can’t interfere visually or interactively. If you’re creating a story-driven animation or a phased visualization, this helps you make it clear which components matter at each step.
Getting started
It’s simple to try:
- Select the atoms and bonds you want to gradually conceal.
- Open the Animation panel in SAMSON.
- Double-click on the Conceal atoms effect.
- Adjust the timing of the 4 keyframes to match your story flow.
You can also choose how the disappearance unfolds by changing the easing curve, giving you finer control over the pacing of the animation. A fast-ease-in, for example, might highlight urgency or abrupt change, while a soft ease-out could create a more natural fade that mimics biological processes.
See it in action
Here’s an example from the documentation, showing both the Conceal and Reveal animations combined in a short loop:
Examples you can download
- 1AF6 – Fly around: A tour around a molecule using reveal and conceal to guide attention.
- 1AF6 – Fly around – 2: A variation emphasizing different structural regions.
Combining Conceal atoms with other animations like Appear, Show, and Reveal allows you to create more complex visual narratives. You can progressively present functional regions of a protein, demonstrate a mutation’s impact, or even create molecular puzzles for educational use.
To learn more about this animation technique, visit the Conceal atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.