If you’ve ever tried to showcase a molecular mechanism and found that parts of your system simply vanish from your animation — and never return — you’re not alone. One common pain molecular modelers face is correctly animating components that need to disappear and then become visible again later in the sequence. Relying only on transparency or other visual effects may not produce the desired result, especially in scientific presentations where clarity is key.
This is where the Shown animation feature in SAMSON comes in. It allows users to control the visibility of nodes (atoms, molecules, or groups) between keyframes. Unlike effects that change transparency, the Shown animation directly toggles the visibility status, clearly reintroducing components at specific moments in your animation timeline.
What Does the Shown Animation Do?
In brief, the Shown animation makes selected nodes appear at a certain point without using semi-transparency. This is particularly useful for complex, multi-step animations where key atoms or molecules return into focus after being hidden or removed in earlier scenes.
Consider, for example, a catalytic process in which a ligand binds, dissociates, and later returns. Using transparency-based transitions, it might be difficult to distinguish between partial visibility and complete reentry. With Shown, the ligand is either there — or it isn’t.
How to Use It
The process is straightforward:
- Select the nodes (components such as atoms, molecules, or groups) you’d like to reintroduce.
- Double-click on the Shown animation effect in the Animation panel.
- A beginning keyframe is automatically set at the current frame. You can move this keyframe to control exactly when visibility begins.
- Adjust the keyframes to fine-tune the timing of reappearance throughout your animation.
Tip
You can always move and stretch the keyframes on the animation timeline to synchronize with other animated events, such as rotations or zooms.
Why Visibility Instead of Transparency?
Transparency works fine if you just want to gradually fade a molecule in or out, but visibility allows for a more definitive approach, making it easier to focus your viewer’s attention. In scientific communication, reducing ambiguity is often more effective than adding visual flourish.
Flexible Controls
You can adjust how the visibility is interpolated across keyframes by modifying the easing curve. For instance, you can make a component suddenly appear (no interpolation) or smoothen the transition for stylistic purposes when combining with opacity-based effects.
The image below illustrates an animation where components enter and exit the scene using both Shown and Hidden effects:
With just a few clicks, you can ensure essential parts of your system reappear exactly when needed, improving storytelling and scientific clarity in your animations.
To learn more, visit the SAMSON documentation on the Shown animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.