Creating effective molecular animations often involves more than just showing or hiding entire structures. A common challenge among molecular modelers is presenting complex mechanisms or transitions without overwhelming the viewer. One useful way to guide attention is to progressively conceal atoms and bonds—without changing their transparency—to introduce or phase out molecular components in a smooth and controlled way.
The Conceal atoms animation in SAMSON provides a built-in solution to this. Instead of shifting transparency levels, it works by toggling the visibility of atoms and the bonds between them—entirely removing them from view over time.
Why conceal instead of fade?
Transparency changes can sometimes leave a ghost-like presence of atoms, which may clutter your animation, especially in dense systems. In contrast, progressive concealment avoids visual noise and focuses a viewer’s attention where it matters. It’s also more computationally efficient, and predictable across diverse backgrounds or rendering styles.
How it works
You can easily add this effect using Animator and the Animation panel. Here’s how:
- Select the atoms and bonds that you want to fade out of your scene.
- Double-click on the Conceal atoms effect in the Animation panel.
- This creates an animation with 4 keyframes:
- Keyframes 1–2: All selected atoms and bonds are visible.
- Keyframes 2–3: Elements progressively disappear based on their order in your current selection.
- Keyframes 3–4: All selected atoms and bonds are hidden.
- Adjust the timing of these keyframes to suit the pace of your animation.
Customize the feel of motion
By modifying the easing curve, you can control how smoothly or abruptly the disappearance unfolds. This helps tailor the animation to different presentation goals—whether you’re showing a rapid transition or a slow unveiling.
Example in action
The GIF below demonstrates the Conceal atoms and Reveal atoms animations working together to focus the viewer’s attention as needed:
Use case: streamlining educational content
Whether you’re illustrating protein folding, ligand docking, or simply cleaning up a crowded binding site, gradually hiding unneeded atoms helps keep your message clear. For example, in presentations like 1AF6 – Fly around, the technique makes it easier to animate molecular landscapes without distraction.
To learn more and explore related animations, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.