When preparing molecular animations or creating visual presentations, clarity is essential. Too many atoms or complex visualizations can make it difficult for a viewer to focus on the message a molecular modeler wants to convey. This is especially true for educational content, conference presentations, or simply for highlighting specific molecular interactions or mechanisms in a video.
One common pain for molecular modelers is how to dynamically simplify a structure without losing important information. In static visuals, atoms can be hidden manually or made transparent—but in optimized, animated storytelling, a smoother transition is often needed. This is where SAMSON’s Conceal atoms animation offers a helpful solution.
What does “Conceal atoms” do?
The Conceal atoms effect in SAMSON gradually makes atoms (and the chemical bonds between them) disappear over a set of animation frames. It does so by changing their visibility, not just their transparency. This creates a clean and sharp effect that avoids visual clutter and highlights what matters most in your animation.
For example, if you’re showcasing ligand binding, protein folding steps, or a catalytic mechanism, the Conceal atoms animation lets you remove less-relevant parts of the molecule over time—without overwhelming the viewer with sudden changes.
How it works
Once you’ve selected the atoms and bonds you’d like to gradually hide, you can apply the Conceal atoms animation through SAMSON’s Animation panel in the Animator. This effect is organized into four keyframes:
- Between keyframes 1 and 2, the selected atoms and bonds are visible.
- Between keyframes 2 and 3, a progressive disappearance occurs.
- Between keyframes 3 and 4, all selected atoms and bonds are hidden.
The order of progressive hiding depends on the atom order in your selection, giving you control over the disappearance sequence. This makes it easier to coordinate the atom hiding with your narrative flow.
Why not just use transparency?
While transparency can also be useful, it still leaves atoms on-screen and sometimes ends up making scenes harder to interpret. The Conceal atoms effect literally removes them from visibility, allowing the viewer to focus only on what’s relevant without distraction.
Customization and easing
The pace of the animation can be adjusted by moving the keyframes, and the transition itself can be controlled more precisely using different easing curves. Whether you want an abrupt or smooth evolution, this added control allows you to fully tailor the viewer experience.
Try it out through examples
SAMSON Connect offers example presentations using this animation. These can help you understand how the effect behaves in the context of a more complex scene:
If your goal is to simplify complex molecular structures in a way that keeps your audience engaged and focused, the Conceal atoms animation is a precise tool to experiment with. It requires no scripting and fits directly into SAMSON’s animation workflow.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.