Presenting complex molecular data in a clear and engaging way can be a challenge—especially when trying to communicate how molecular assemblies form or identifying the focus of a transition. Whether you’re giving a scientific presentation, building educational content, or preparing a publication, you often need to emphasize specific atoms or regions of interest incrementally across frames.
One common problem is the need to show atoms and their bonds progressively, without distracting effects like full transparency or abrupt changes that obscure the transition’s meaning. That’s where the Reveal atoms animation in SAMSON can help.
What is the Reveal Atoms Animation?
The Reveal atoms animation allows you to gradually show selected atoms and the bonds between them as the animation advances. Rather than playing with transparency, which can sometimes result in visual clutter or confusion, this animation works by adjusting visibility. This approach offers better control in visually guiding a viewer’s attention.
Where This Becomes Useful
You might find yourself in one of these scenarios:
- You’re demonstrating the assembly of a protein complex.
- You want to progressively highlight an active site or ligand-binding pathway.
- You want the audience to focus sequentially on specific atoms during molecular training or lectures.
In each case, showing everything at once can be overwhelming or confusing. A gradual build-up makes things easier to follow and more visually engaging.
How It Works
After selecting the atoms and bonds you want to reveal, simply double-click “Reveal atoms” in SAMSON’s Animation panel. This animation introduces 4 keyframes that oversee the process:
- Keyframes 1 to 2: All selected atoms and bonds are hidden.
- Keyframes 2 to 3: Atoms and bonds progressively appear based on their selection order.
- Keyframes 3 to 4: All selected atoms and bonds are fully shown.
This flow gives you control not only over what is revealed but also when and how fast.
Tweaking Transitions
The timing of transitions can also be fine-tuned with easing curves, allowing you to control the rate of visibility changes—whether it’s a smooth start, a linear reveal, or quick bursts. These small adjustments can make a big difference in clarity and impact.
Animated Example
Here’s how this looks in action:
Final Tip: Combine Animations
For even more control, consider combining “Reveal atoms” with the complementary “Conceal atoms” animation. This lets you organically move between fully hidden and fully shown views to create smooth, narrative-style molecular demonstrations.
Visit the Reveal atoms documentation page to learn more.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.