When creating presentations or educational content about molecular structures, researchers and educators face a recurring challenge: how to progressively guide the viewer’s focus without overwhelming them visually. Showing every part of a molecule at once—especially complex biomolecules like proteins or nucleic acids—can distract rather than communicate. One practical way to address this is to make certain atoms and bonds progressively disappear from the scene, helping the viewer focus step-by-step.
The Conceal Atoms animation in SAMSON, the integrative platform for molecular design, offers exactly this capability. It helps you simplify a molecular scene during an animation by hiding selected atoms and bonds not by fading them out, but by actually making them disappear completely between two specific timepoints in your animation sequence.
Why hide instead of fade?
The Conceal Atoms effect works by adjusting the visibility of selected nodes (atoms and bonds), rather than adjusting their transparency. This distinction is important. Transparency may still leave molecular fragments visible, contributing to visual noise. Visibility control, on the other hand, lets you cleanly remove them from the scene in an ordered, frame-dependent way.
How it works
When applied through the Animation Panel in SAMSON’s Animator, the Conceal Atoms effect inserts four keyframes into your animation timeline:
- Keyframe 1→2: All selected atoms and bonds are visible and persist unchanged.
- Keyframe 2→3: The selected atoms and bonds progressively disappear based on their order in the selection list.
- Keyframe 3→4: All those atoms and bonds are now hidden.
This structure gives you tight creative control over how and when each part of a molecular structure vanishes, creating a natural transition for slidedecks, videos, or exploratory molecular storytelling.
When to use this animation
This effect is especially useful when you want to:
- Transition from a whole-molecule view to an active site or pocket
- Unveil internal structures by stripping away exterior components
- Show comparison stages in a simulation where parts of the molecule vanish (e.g., docking or unfolding processes)
You can pair this effect with the corresponding Reveal Atoms animation to reintroduce parts later in your animation. This combination (Conceal → Reveal) is shown in the animation below:
Customization tips
You can fine-tune how the atoms disappear by modifying the Easing curve. This defines how the speed of the concealment evolves over time—linearly or with acceleration or deceleration.
Looking for real-world usage examples? Several shared documents on SAMSON Connect showcase this approach in action. For example:
If you’re designing a molecular presentation that needs to manage complexity with clarity, Conceal Atoms is an effective and easy-to-use approach. Build transitions that guide attention without relying on complicated transparency channels.
Learn more from the original documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.