When preparing molecular presentations or animations in SAMSON, a common challenge is transitioning smoothly from invisible to visible structural elements. Rather than having parts of your molecular model snap instantly into view, a progressive appearance helps direct attention and improves clarity, especially during tutorials or collaborative sessions.
This is where the Appear animation in SAMSON’s animation panel is especially useful. It allows any nodes that support transparency—such as structural models, visual models, meshes, and labels—to fade into the scene gradually. If you’ve struggled to guide an audience through complex structures without overwhelming them, this animation can help by providing a cleaner visual flow.
Why use the Appear animation?
Imagine you’re building an educational demo on protein-ligand docking. Instead of abruptly displaying the entire protein, you could progressively reveal the ligand binding pocket. Or, when introducing surface meshes around molecules, slowly increasing their opacity avoids overwhelming the viewer with too much detail at once.
By transitioning from full transparency to full opacity, the Appear animation adds a layer of polish while also serving a functional role: focusing attention and improving visual understanding.
Applying the animation step-by-step
- Select the nodes you want to animate (e.g., a structural model).
- Open the Animation panel in SAMSON’s Animator.
- Double-click the Appear animation effect.
The animation comes pre-loaded with 4 keyframes:
- Keyframes 1–2: Nodes remain fully transparent.
- Keyframes 2–3: Transparency decreases progressively.
- Keyframes 3–4: Nodes become fully opaque.
You can drag keyframes to adjust timing and pacing. If a slower fade-in helps emphasize a structural point, simply expand the time interval between keyframes 2 and 3.
Refining the appearance with easing curves
To make transitions even smoother, SAMSON allows you to set easing curves. This means you can control how quickly or slowly the transparency changes between keyframes—giving you more flexibility to match the animation’s pace with your narration or audience needs.
What about atoms and bonds?
It’s important to mention that individual atoms and bonds don’t have a transparency property. To animate them using Appear, apply the animation to their parent structural model. This still gives you the visual effect of atoms and bonds fading in.
Example in action
Here’s a visual example showing the combined use of Appear and Disappear animations to transition objects in and out of view smoothly:
Animations like Appear are small touches that can make molecular storytelling clearer and more engaging. In teaching, documentation, or scientific presentations, they help structure the visual flow of information to match what you’re explaining.
To learn more about the Appear animation, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/appear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.