In molecular modeling and simulations, visualizations are essential for storytelling. Whether you’re preparing a conference talk, sharing a molecular mechanism on social media, or teaching students about molecular interactions, how you present your model can affect understanding and engagement.
One common need arises when emphasizing specific regions of a molecule or showing sequential assembly or disassembly: you want some atoms to disappear in a controlled, progressive manner. Instead of abruptly hiding atoms or using transparency overlays, which can confuse viewers, SAMSON’s Conceal atoms animation offers a more deliberate and elegant solution.
Why hide atoms progressively?
Let’s say you’re explaining an active site buried within a protein. If all surrounding atoms suddenly vanish, your audience might lose context or orientation. A progressive concealment lets them follow the transformation step-by-step, maintaining spatial awareness and focus. It works well for:
- Revealing binding pockets or ligand interactions
- Showing structural changes over time
- Layering educational content for students new to structural biology
How Conceal Atoms works
Unlike transparency-based effects, the Conceal atoms animation in SAMSON uses the visibility of nodes, making atoms and bonds disappear systematically over a specific interval. This provides a crisper and computationally simpler outcome, especially for large molecules.
You add the animation by selecting atoms and bonds in your molecular model, then double-clicking Conceal atoms in the Animation panel. The animation plays across 4 keyframes:
- Keyframes 1–2: All selected atoms and bonds are fully visible.
- Keyframes 2–3: Atoms and bonds progressively disappear, based on their order of selection.
- Keyframes 3–4: All selected atoms and bonds are fully hidden.
Keyframes can always be adjusted to fine-tune timing and rhythm. For added aesthetic control, modify the Easing curve to change how the animation interpolates over time—linear, quadratic, or more complex profiles.
Use case examples you can explore
To see how creators are incorporating this animation into molecular storytelling, check out these sample presentations on SAMSON Connect:
These examples showcase progressive unveiling workflows often used in active site exploration and other molecular animations.
Visual example
Thoughtfully hiding atoms can do more than just clean up a view—it can make your molecular story clearer.
For full instructions and options, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net