One common challenge in molecular modeling is how to clearly communicate structural changes or dynamic behaviors, especially when dealing with crowded molecular scenes. Important insights can be hidden in a cluster of atoms or overwhelmed by visual complexity. The Conceal atoms animation effect in SAMSON offers an elegant solution: it lets you progressively hide atoms and the bonds between them, helping focus attention where it matters most.
This animation doesn’t rely on transparency, but rather on a change in visibility – making it especially useful in educational content, presentations, or collaborative design efforts where clarity is critical.
What Does It Do?
With the Conceal atoms animation, you select a group of atoms and bonds, and make them progressively disappear over time, between specific frames in your animation. This effect can help achieve several objectives:
- Clean up molecular assemblies gradually to focus on active sites or interactions.
- Illustrate sequential processes at the atomic scale.
- Improve storytelling in molecular presentations.
How It Works
In the Animator module in SAMSON, you’ll find the Conceal atoms effect in the Animation panel. After selecting the atoms and bonds you want to progressively hide, simply double-click the animation effect to apply it. It comes with four keyframes:
- Between keyframes 1 and 2: All selected atoms and bonds are fully visible.
- Between keyframes 2 and 3: Atoms and bonds progressively disappear based on their selection order.
- Between keyframes 3 and 4: All selected atoms and bonds are fully hidden.
You can move these keyframes along the timeline to fine-tune the pacing of the effect.
Adjusting the Transition
If you want more control over how fast or slow the atoms conceal at any point in time, modify the Easing curve. This lets you add smooth acceleration, deceleration, or even non-linear behavior to the animation.
When to Use It
The Conceal atoms effect is particularly useful when dealing with simulations, large biomolecular complexes, or when trying to compare structural states. Instead of showing everything at once, which can overwhelm a viewer, this approach guides the eye progressively.
Visual Example
The following animation demonstrates how atoms and bonds progressively disappear using the effect:
See It in Action
If you want hands-on examples, check out documents on SAMSON Connect that use this effect, such as:
Conclusion
If you’re tired of visually cluttered molecular animations, the Conceal atoms tool may help you create more focused and engaging visualizations. Whether it’s for research communication or instructional videos, smartly hiding parts of your model can sometimes tell a clearer story than showing everything.
Learn more by visiting the Conceal atoms documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.