In molecular modeling and presentations, visibility isn’t just about zooming or panning—it’s often about knowing what to show and when. A common obstacle faced by researchers and educators is how to direct focus within complex molecular structures. Showing too much at once can overwhelm your audience. But what if you could control which atoms fade out of view, guiding attention step-by-step?
That’s where the Conceal atoms animation in SAMSON comes into play. With this animation feature, you can progressively hide selected atoms and the bonds between them during a molecular animation. Unlike classic fading, which relies on changing transparency, this effect works by adjusting the visibility of nodes. This can be especially helpful when creating visually clean and pedagogically effective molecular demonstrations.
Why gradually hide atoms?
There are several cases in which progressive concealment helps:
- To transition between different levels of structural detail (e.g., from full atomistic to backbone-only views).
- To isolate active or binding sites.
- To sequentially introduce interactions or domains in a complex system.
- To focus an audience’s attention in educational contexts.
How it works in SAMSON
Setting up a Conceal atoms animation is straightforward. Here’s a step-by-step summary:
- Select the atoms and bonds you want to hide progressively.
- In the Animation panel of the Animator, double-click on the Conceal atoms animation effect.
- SAMSON will automatically create four keyframes:
- Keyframe 1 to 2: Atoms and bonds are fully shown.
- Keyframe 2 to 3: Progressive concealment based on the selection order.
- Keyframe 3 to 4: All specified atoms and bonds are fully hidden.
- You are free to move the keyframes to control the timing and rhythm of the transition.
Fine-tuning your animation
If you want to adjust how smoothly or abruptly the hiding happens, SAMSON allows you to modify the Easing curve. This means you can set the animation to start slowly and finish quickly, or vice versa, fine-tuning the pacing to match your narration or visual storytelling.
Want to see it in action?
You can find concrete examples using this effect, such as:
The Conceal atoms animation is one of SAMSON’s many tools designed to help you clearly communicate molecular features. Whether you’re preparing a publication-grade visualization, teaching a class, or designing an interactive demo, the ability to hide regions of a molecule gradually provides valuable control over how your audiences perceive structure and functionality.
To learn more and try it yourself, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.