When creating molecular animations to educate, explain, or discover, one of the biggest challenges is guiding the viewer’s attention. In complex molecular systems, every atom and bond contributes to visual clutter. But what if you could make selected atoms gently disappear — without abruptly cutting them out or adjusting transparency sliders?
The Conceal atoms animation effect in SAMSON offers a streamlined way to progressively hide atoms and bonds between them. Instead of visually fading elements using transparency, this effect directly controls visibility, ensuring smooth and performant rendering during your presentations or animations.
Why Visibility Instead of Transparency?
Modelers often resort to transparency when trying to emphasize selected parts of a molecule. However, transparency:
- Still renders geometry, consuming GPU power
- Can result in visual noise due to overlapping semi-transparent elements
- Makes selection more complicated when editing the model interactively
Using visibility to conceal atoms altogether is often clearer and computationally simpler. Plus, the progressive concealment via animation creates a clean, elegant transition.
How It Works in SAMSON
The Conceal atoms effect is part of the Animation panel in the Animator module. Here’s what happens internally:
- Between keyframes 1 and 2: the selected atoms and bonds are visible.
- Between keyframes 2 and 3: atoms and their connecting bonds are progressively hidden in the order defined by the selection order.
- Between keyframes 3 and 4: all those atoms and bonds are fully hidden.
You can tailor the entire effect dynamically by repositioning the keyframes. This makes timing the concealment with narration or interaction much easier.
Easing Curves: Making It Smoother
Don’t want a linear pace of concealment? Open the animation properties and tweak the easing curve. This gives you control over acceleration—allowing atoms to vanish slowly at first and then faster, or vice versa. The right curve can elevate your animation’s clarity without adding complexity.
See It in Action
Here’s an example of how it looks when combined with a reverse effect (reveal):
When to Use This
Modelers frequently use the Conceal atoms effect when:
- Focusing on a ligand binding site by hiding the surrounding protein structure
- Transitioning between structural states (e.g., from full protein to domain-specific views)
- Visually segmenting parts of an assembly without overwhelming the viewer
In combination with other animation effects like Reveal atoms or Flash, you can craft compelling educational videos or step-by-step demonstrations.
Want to Try It?
Example presentations using the Conceal atoms animation include:
To learn more, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.