Creating compelling molecular animations is often an overlooked challenge for researchers and educators who aim to explain complex processes like ligand binding, protein folding, or chemical reactions. One common pain point is the need to visually remove unnecessary elements from a molecular scene in a way that is neither abrupt nor jarring.
This is where the Conceal atoms animation from the SAMSON molecular design platform comes in. Instead of making atoms transparent or suddenly disappearing, Conceal atoms offers a smoother, more controllable transition: atoms (and the bonds between them) progressively vanish between two keyframes based on their selection order. This can help direct the viewer’s attention and make molecular processes more intuitive to understand.
Why progressive disappearance matters
Images and animations play a vital role in scientific communication. Imagine a presenter discussing an active site in a protein while irrelevant parts of the molecule clutter the scene. Just hiding irrelevant atoms may appear too abrupt, and transparency may add visual noise. The Conceal atoms animation makes transitions smoother and more controlled by managing visibility keyframes — without affecting transparency settings. It shows viewers what’s important, then seamlessly clears the rest.
How it works
To use this effect, select the atoms and bonds you want to gradually remove. Then apply the Conceal atoms effect by double-clicking it in the Animation panel of the Animator. The effect is structured around four keyframes:
- Keyframes 1 → 2: All selected atoms and bonds remain visible.
- Keyframes 2 → 3: Selected atoms and their internal bonds begin to disappear progressively in the order of selection.
- Keyframes 3 → 4: Final state — all selected components are hidden.
You can freely move these keyframes along the animation timeline to tailor the transition speed. This flexibility makes it suitable for building interactive presentations or explanatory videos — great for both scientific talks and classroom content.
Presentation examples
If you’d like to see the Conceal atoms effect in action, here are two accessible demonstration documents:
These examples highlight how selectively removing parts of a molecular model can bring more focus to the underlying mechanisms without visual overwhelm.
Tune the ease of transition
You’re not limited to a linear disappearance. Adjust the Easing curve to make the change fast or slow, or apply other curve shapes to dramatize or soften the removal action. This small tweak can significantly impact the user experience, especially in guided or educational videos.
To learn more about this animation, visit the original documentation page: https://documentation.samson-connect.net/users/latest/animations/conceal-atoms/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.