When presenting molecular models, clarity and engagement matter. Static images or rigid transitions can sometimes make it difficult to convey the dynamics of complex molecular assemblies. If you’ve ever struggled to draw attention to specific parts of your molecular model without overwhelming your audience or cluttering your animation, SAMSON’s Pulse animation might be the tool you’ve overlooked.
The Pulse animation provides a smooth, rhythmic way to emphasize parts of a molecular system—making them appear and then gently disappear—without jarring transitions. This is especially useful when you want your audience to focus on specific nodes, such as structural or visual models, or even meshes and labels that support transparency.
Why Use the Pulse Animation?
One common challenge in molecular visualization is directing focus while preserving overall context. The Pulse animation solves this by:
- Gradually guiding the viewer’s eyes to key components in the structure.
- Reinforcing rhythmic transitions in presentations (ideal for loops or repeated motifs).
- Reducing cognitive load with smooth transparency changes.
The visual effect mimics a breathing rhythm, quite literally making your models feel alive, which can be particularly helpful for communicating concepts like structural conformations, ligand binding sites, or compartmentalized dynamics.
How It Works
To apply the Pulse animation in your project:
- Select nodes that support transparency (e.g., structural models, visual models, meshes).
- Open the Animation panel in the Animator.
- Double-click on Pulse to apply the effect to the selected nodes.
The animation consists of five keyframes:
- Frames 1-2: Full transparency (nodes are invisible).
- Frames 2-3: Transparency decreases; nodes gradually appear.
- Frame 3: Full opacity (nodes completely visible).
- Frames 3-4: Transparency increases; nodes begin to fade.
- Frames 4-5: Full transparency again.
You can customize the timing by moving the keyframes to speed up or slow down the cycle according to your narrative.
Adjusting the Easing Curve
The subtlety of the Pulse effect can be fine-tuned even further. By editing the easing curve in the Inspector panel, you control how quickly or slowly the transparency changes between frames. This makes it possible to make the transitions feel soft or sharp depending on your scientific storytelling needs.
When to Use It
While the Pulse animation is not suitable for every scenario, it excels in illustrative or educational contexts where rhythmic emphasis on molecular components helps communicate function, interaction, or periodicity. Here are a few use cases:
- Showing active sites or binding pockets in large assemblies.
- Highlighting repeated structural elements (e.g., helices or beta-sheets).
- Creating loops for background animations during poster sessions or video lectures.
The Pulse animation is a lightweight but effective tool to make your molecular models more expressive without adding complexity.
To learn more or explore related animations such as Appear, Disappear, Flash, and others, visit the official documentation page: 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.