When creating molecular presentations or videos, one recurring challenge is helping viewers understand the step-by-step buildup of complex molecular structures. Rather than showing everything all at once—which can be overwhelming—it can be much more effective and pedagogical to have components appear progressively, guiding the observer’s attention.
This is exactly what the Appear animation in SAMSON enables.
Why use the Appear animation?
Whether you’re presenting a structural model to peers, teaching students about biomolecular organization, or walking through the stages of a docking simulation, visually controlling how content is introduced makes a substantial difference in comprehension and engagement.
The Appear effect lets selected nodes (e.g., molecular models, meshes, or labels) begin completely transparent and gradually become opaque. This transparency-based animation extends beyond simple show/hide actions and adds subtlety to molecular storytelling.
What kinds of nodes can use Appear?
This animation can only be applied to nodes that feature a transparency attribute. These include:
- Structural models
- Visual models
- Meshes
- Labels
Note that individual atoms and bonds do not have their own opacity attributes. If you want to animate them, apply the Appear effect to their parent structural model.
How it works in SAMSON
To use the Appear effect:
- Select the nodes you want to animate.
- Double-click the Appear animation effect in the Animation panel of the Animator workspace.
This animation uses 4 keyframes that define the stages of the transition:
- Keyframes 1 → 2: Nodes remain fully transparent
- Keyframes 2 → 3: Transparency gradually decreases, nodes start to appear
- Keyframes 3 → 4: Nodes become fully opaque
You can adjust these keyframes along the timeline to control the duration of each phase. For more advanced control, the easing curve lets you fine-tune how quickly the opacity transitions occur.
Example: Animation in action
Here is a GIF example where Appear and Disappear effects are used for smooth visual transitions:
Tip for presenters
To avoid confusion: the movie above uses an older Animation menu that has since been replaced. Today, all animations are accessible through the Animation panel in the Animator module (shortcut: Ctrl + 7 on Windows / Cmd + 7 on macOS).
Using the Appear effect adds gentle flow to your molecular animations, keeping your audience focused and making your presentations more intuitive.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.