When presenting molecular models, clarity and elegance go hand in hand. But if you’ve ever tried to represent dynamic states—highlighting or fading specific parts of a complex structure over time—you’ve likely wondered how to do this smoothly and repeatedly without constant manual adjustments.
This is where the Pulse animation effect in SAMSON can help. It solves a common presentation pain for molecular modelers: how to make parts of a model appear and disappear in a continuous, eye-catching loop. This can be especially useful for highlighting binding sites, visualizing conformational cycles, or drawing attention to specific substructures without resorting to abrupt toggles or cluttered overlays.
What is the Pulse Animation?
The Pulse animation creates a rhythmic, smooth transition where nodes appear (by decreasing their transparency), become fully opaque, and then fade out again (by increasing their transparency). This kind of visual signaling can elevate molecular storytelling, making your animations more intuitive for viewers.
It is particularly effective when applied to any node that has transparency attributes, including:
- Structural models
- Visual models
- Meshes
- Labels
How to Add the Pulse Effect
Applying the Pulse effect is simple, but understanding how it works helps you get the most out of it. Here’s a breakdown:
- Select the nodes you want to animate—these could be parts of a protein, ligands, labels, or visuals you’ve added to help explain a concept.
- Open the Animation panel via the Animator.
- Double-click the Pulse animation from the list of effects.
Once added, the animation will contain five keyframes:
- Keyframes 1–2: The nodes remain fully transparent.
- Keyframes 2–3: Nodes fade in until they are fully opaque.
- Keyframe 3: Nodes are fully visible.
- Keyframes 3–4: Nodes fade out back to transparency.
- Keyframes 4–5: Nodes remain fully transparent again.
You can reposition these keyframes on the timeline to accommodate the rhythm or pace you want—whether a quick flicker or a slow, gentle pulse.
Advanced Tip: Adjust Easing for Even Smoother Results
Want your fades to feel more organic or more mechanical? Modify the Easing curve to change how rapidly nodes fade in or out between frames. This lets you craft exactly the effect you’re after, whether it’s a linear pulse or one that accelerates or decelerates at different moments.
Why Use Pulse?
Animations like Pulse aren’t just “visual candy.” In fields like drug design, structural biology, and bioinformatics, clearly communicating which molecular parts are active, intermittent, or emerging across states is critical. Pulse provides a clear, professional-looking way to draw attention over time, reducing the cognitive load on your audience.
For more details, visit the official Pulse animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.