When creating molecular animations for teaching, presentations, or publications, one common challenge is how to focus viewers’ attention on specific parts of a complex scene. Simply showing everything at once can overwhelm the viewer, making it difficult to follow the scientific story you want to tell.
The Pulse animation in SAMSON offers a simple and effective solution: it brings molecular nodes into view, then fades them away in a looping, eye-catching animation. This can help viewers notice features that would otherwise be buried in static visualizations.
Why Use Pulse Animations?
Animations aren’t just about making science look good—they’re about communication. With the Pulse effect, you can:
- Guide attention to structures (e.g., receptor binding sites, mutations, ligands, or nanoscale features)
- Repeat visibility cycles to emphasize recurring processes
- Discretely show and hide labels, meshes, or visual models without cluttering your scene
The Pulse animation is designed for nodes that support transparency—common examples include structural models, visual models, labels, and meshes.
How Does It Work?
After selecting your nodes, you just double-click the Pulse animation effect in the Animation panel. This creates a timeline with five keyframes that define the cycle:
- Keyframes 1–2: Fully transparent nodes
- Keyframes 2–3: Gradual appearance (transparency decreases)
- Keyframe 3: Fully opaque (max visibility)
- Keyframes 3–4: Gradual disappearance (transparency increases)
- Keyframes 4–5: Fully transparent again
This structure is well-suited for highlighting events in ongoing biological processes or repeating emphasis across a sequence. You can always move the keyframes to change timing and adapt to your scene.
Fine-Tuning the Effect
To adjust how the visual change occurs, modify the easing curve in the Inspector. This controls how fast or slowly the transparency values change between two keyframes. For example, you could make the fade-in fast and the fade-out slow, or vice versa.
When to Use (and Not to Use)
The Pulse effect works best for scenes involving a few focused elements. Overusing it across a large number of structures can be visually chaotic. Instead, consider combining it with other animation types (like Flash or Show) for contrast and variety.
Animations can also be layered, enabling you to coordinate different emphasis effects across a timeline. With practice, you’ll find subtle ways to guide attention through molecular stories using animation structure and timing alone.
Learn more about Pulse animations in the full documentation here:
https://documentation.samson-connect.net/users/latest/animations/pulse/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.