When giving scientific presentations or creating molecular animations, researchers often face the challenge of controlling visual clutter. Showing complex molecular systems in their entirety can overwhelm an audience and obscure the main points. Yet fully hiding parts of a model can appear abrupt and disorienting.
To address this, the Disappear animation in SAMSON offers a simple way to gradually fade out molecular elements, guiding viewers’ attention without breaking the visual flow. It’s especially useful when you want parts of a system to leave the scene subtly while keeping the overall tempo of an animation sequence smooth and uninterrupted.
Why not just “Hide”?
Hiding elements makes them instantly disappear, which may not reflect realistic physical transitions like molecular diffusion or systematic de-emphasis during a step-wise mechanism illustration. A fading effect—made possible by the Disappear animation—preserves continuity and reduces visual shock, especially when animating complex assemblies.
What the Disappear animation does
The Disappear animation works by modifying the transparency of nodes, progressively increasing their transparency over time. This only applies to node types that have a transparency attribute, such as:
- Structural models
- Visual models
- Meshes
- Labels
It’s important to note that atoms and bonds don’t have individual transparency attributes; the animation must be applied to their parent structural model nodes.
How to use it in SAMSON
To add the Disappear animation:
- Select the nodes you want to fade out.
- Open the Animator.
- Double-click on Disappear in the Animation panel.
This inserts four keyframes:
- Between frames 1 → 2: the nodes remain fully visible (opaque).
- Between frames 2 → 3: transparency progressively increases.
- Between frames 3 → 4: the nodes are fully transparent.
By dragging the keyframes along the animation timeline, users can precisely control the timing of the fade-out effect. For even more customized animations, SAMSON supports modifying the easing curve to produce different rates of transition.
A common use case
Imagine animating the binding of a ligand to a protein. After the binding step, you may want to fade out the solvent molecules to focus the viewer’s attention on the active site. Instead of instantly hiding the solvent, you apply the Disappear effect to their structural model. The gradual fade gives the audience time to visually process the abstraction while still understanding what is being removed from the scene.
This animation effect is a small detail that can make a big difference in the clarity of molecular presentations, especially for educational settings or interdisciplinary collaborations.
To learn more, visit the official Disappear animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.