When presenting complex molecular systems, clarity matters. Molecular modelers often face the challenge of showing transitions or drawing attention to specific molecular components without overwhelming the viewer with visual clutter.
One common pain point is how to illustrate the step-by-step removal or transformation of atoms in a structure. Whether you’re highlighting the effect of a chemical reaction, showing structural simplification, or guiding viewers through a molecular narration, the problem remains: how can you make atoms disappear clearly and gradually—without confusing your audience?
Enter the Conceal atoms animation effect in the SAMSON platform. This tool allows molecular modelers to make atoms and their connecting bonds disappear progressively between animation frames. Unlike transparency, which simply fades objects, this animation reduces visual complexity by actually hiding atoms and bonds over time.
What makes it different?
While many tools use alpha transparency to create the illusion of disappearance, SAMSON’s Conceal atoms animation works by toggling visibility. This method ensures higher rendering performance (especially for large molecules) and provides a cleaner, less cluttered result—particularly useful in educational and scientific storytelling.
How it works
To apply the effect:
- Select the atoms and bonds you want to make disappear over time.
- Open the Animation panel in the Animator.
- Double-click the Conceal atoms effect. This creates a 4-keyframe animation track.
Breaking down the keyframes
- Keyframes 1 → 2: All selected atoms and bonds are fully visible.
- Keyframes 2 → 3: Atoms and bonds start to disappear progressively. Elements are hidden following the order in your selection.
- Keyframes 3 → 4: All the selected atoms and bonds are fully hidden.
You’re free to move any keyframe to adjust timing and pacing. For smoother visual effects, you can also tweak the Easing curve, which controls how the concealment accelerates or decelerates between frames—allowing for decays that feel linear, exponential, or even more cinematic.
Use cases
This animation is perfect for:
- Demonstrating the gradual breakdown of a compound
- Revealing inner layers of a protein structure with context
- Guided lectures or video presentations that focus attention
You can see this feature showcased in animated presentations like:
With these tools, your animations can do more than just look good—they can also tell better molecular stories.
To learn more about how to use this feature, check out the official documentation here: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.