When preparing presentations or videos of molecular systems, one common challenge is smoothly introducing atoms—especially when showcasing molecular docking, assembly, or reaction mechanisms. Instead of showing everything at once or relying on fades, you might want atoms and their bonds to appear step-by-step as the simulation progresses.
This is exactly what the Reveal atoms animation effect in SAMSON helps solve. Whether you’re building educational content, sharing simulations with collaborators, or preparing a research conference video, you can now animate atom appearances in a more intuitive way.
Why Not Just Use Transparency?
While transparency effects can fade atoms in or out, they don’t always feel precise. In structural biology, it often matters what is visible and when. The Reveal atoms effect handles visibility directly: atoms and bonds are shown or hidden cleanly, without relying on transparency levels. This gives you greater visual control over molecular storytelling.
How the Reveal Atoms Effect Works
The Reveal atoms animation is applied from the Animation panel in the Animator workspace. Here’s how it works:
- Step 1: Select the atoms and bonds that you would like to animate.
- Step 2: Double-click the Reveal atoms animation effect in the Animation panel.
The effect comes with 4 keyframes:
- Keyframes 1 to 2: All selected atoms and bonds are hidden.
- Keyframes 2 to 3: Selected atoms and bonds progressively appear one-by-one, based on selection order.
- Keyframes 3 to 4: Everything is fully visible.
You can adjust the timing and spacing of these keyframes to control where and how quickly atoms appear. This provides great flexibility for syncing your animation with narration or other overlaid data.
Enhancing with Easing Curves
For smoother transitions between states, SAMSON also lets you change the easing curves—the interpolation between keyframes. This allows you to control not just what appears, but how it appears: linearly, gradually accelerating, or decelerating for dramatic effect.
Example: Conceal and Reveal
Here’s a visual walkthrough of both the Conceal and Reveal atoms animations in action:
In the gif above, you’ll notice how atoms disappear and reappear clearly, one by one, letting viewers follow structural changes step-by-step. This kind of visual clarity is especially valuable when explaining large molecular complexes or highlighting dynamic mechanisms over time.
Small Tweaks, Big Impact
Animation tools like Reveal atoms may seem minor at first. But they help solve a very real pain: communicating complex molecular behavior clearly. Rather than simply showing a static end state, you’re guiding viewers through a molecular story—atom by atom, bond by bond.
To get started or learn more about applying this effect, visit the full documentation here: https://documentation.samson-connect.net/users/latest/animations/reveal-atoms/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download them at https://www.samson-connect.net.