When you’re presenting molecular models, particularly during a talk, an animation, or even while creating educational videos, it’s important to guide your audience’s attention to certain structures without overwhelming them. One common challenge molecular modelers face is how to make complex models more digestible while keeping viewers engaged. The Pulse animation in SAMSON offers a simple yet effective way to do this.
Rather than showing entire molecular structures all at once, the Pulse animation gently fades them in, pauses at full opacity, and then fades them out. The result? A breathing-like effect that can help highlight key objects within your molecular systems — be it structural models, visual models, meshes, or even labels.
The Concept Behind “Pulse”
Think of Pulse as a rhythmic sequence: transparent → visible → transparent. It consists of five keyframes that achieve this transition:
- Keyframes 1-2: The node is fully transparent.
- Keyframes 2-3: Gradual fade-in to full opacity.
- Keyframe 3: Node is fully visible (opaque).
- Keyframes 3-4: Gradual fade-out to transparency.
- Keyframes 4-5: Completely transparent again.
This heartbeat-like cycle can be repeated, delayed, or stacked with other animations (like Flash or Appear) to build layered visual cues in your presentation. It’s especially helpful when multiple elements need their moment on stage without overwhelming the viewer with too much information at once.
How to Apply the Pulse Animation
Once you’ve selected the nodes you want to animate (for example, specific atoms, residues, or annotations), simply open the Animation panel in the Animator, and double-click Pulse.
You can adjust the timing of each keyframe to match the pace of your presentation. Whether you want a slow, meditative breathing pattern or a quick pulse to draw attention, you’re in control.
Fine-Tuning the Pulse
One useful feature for customization is the ability to define how properties like opacity transition over time. This is done through the Easing curve. Whether it’s linear, smooth, or abrupt, the curve shapes the feel of the animation, giving you more creative control.
When to Use It
Here are a few scenarios where Pulse can be especially useful:
- Step-by-step reveals: Demonstrate how ligands bind to an active site.
- Layered insights: Temporarily reveal deeper shells or annotations inside a molecule.
- Focus cues: Keep your audience tuned in by pulsing only the active region.
By subtly guiding your viewers’ attention, Pulse helps make your presentations cleaner and more effective.
To learn more and explore the full capabilities of the Pulse animation, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.