Visual storytelling is essential when presenting molecular structures in a clear and accessible way—whether it’s for educational videos, research presentations, or collaboration. But have you ever had models just suddenly appear on screen, breaking the fluidity of your animation? That jarring effect can distract viewers just when you’re trying to focus their attention.
This is where the Appear animation in SAMSON comes in handy. It allows molecular modelers to make nodes gradually transition into view, making animations feel more polished and easier to follow. This is especially useful when introducing new components step-by-step as part of a larger molecular scene.
Progressive Appearance in Molecular Animations
The Appear animation is designed to smoothly animate the transition from transparency to opacity for elements that support it—like:
- Structural models
- Visual models
- Meshes
- Labels
This subtle shift from invisible to visible can significantly improve how viewers process complex information. It’s especially useful when transitioning between stages of a reaction or focusing on newly added substructures.
Important note: Atoms and bonds themselves don’t have transparency attributes. The transparency must be applied at the level of the structural models that contain them. So always apply the Appear animation to those higher-level nodes.
How It Works
Adding the Appear animation in SAMSON is straightforward:
- Select the nodes you want to animate.
- Double-click the Appear effect in the Animation panel within the Animator.
The animation spans four keyframes:
- Between keyframes 1 & 2: Nodes are fully transparent.
- Between keyframes 2 & 3: Transparency gradually decreases.
- Between keyframes 3 & 4: Nodes are fully opaque.
Timing is flexible—you can always reposition the keyframes to match your presentation’s rhythm. Additionally, SAMSON supports customizable easing curves to control how smoothly the opacity changes over time.
When to Use It
The Appear animation is helpful in scenarios like:
- Step-by-step teaching of protein folding.
- Introducing additive changes in ligand binding.
- Dynamically focusing on functional sites or domains.
It helps guide the viewer’s attention and maintain a logical flow without overwhelming them with visual noise.
To explore additional animation options—like Disappear, Flash, or Pulse—and build more expressive presentations, visit the full Appear documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at www.samson-connect.net.