Give Your Molecules a Heartbeat with the Pulse Animation in SAMSON

Visualizing molecular behavior isn’t just about displaying a static snapshot—it’s about telling a story. Whether you’re preparing a presentation, explaining interactions in your research, or creating content for outreach, dynamic visuals help communicate effectively. But there’s a common challenge faced by molecular modelers and educators alike: how to draw attention to specific parts of complex molecular structures without overwhelming viewers.

The Pulse animation in SAMSON offers a simple but effective solution to this. It provides a smooth animation effect where selected nodes (like molecules, meshes, or labels) gently appear and disappear in a loop—similar to a heartbeat. It’s a subtle tool, but when used correctly, it can bring focus and rhythmic visual flow to your scientific animations.

What Does the Pulse Animation Do?

The Pulse animation works on nodes that support transparency—this includes structural models, visual models, meshes, and labels. With it, selected parts of your scene will fade in and out over time. This can be especially helpful to:

  • Highlight a reaction center or active site in a large biomolecule
  • Indicate orbits or trajectories dynamically in visual models
  • Draw attention to key labels or annotations during a presentation

How Does It Work?

The animation is built using 5 keyframes to define the transparency states over time:

  • From keyframes 1 to 2: nodes are fully transparent
  • From keyframes 2 to 3: nodes fade in
  • At keyframe 3: nodes are fully visible (opaque)
  • From keyframes 3 to 4: nodes fade out
  • From keyframes 4 to 5: nodes are fully transparent again

This loop can easily be adjusted by dragging individual keyframes on the timeline, letting you control the pace and timing of the pulse effect. It’s a very flexible, low-barrier way to enhance your animations.

Quick Guide: Adding the Pulse Animation

  1. Select the nodes you want to pulse (e.g. molecule or label)
  2. In the Animator’s Animation panel, find and double-click the Pulse animation
  3. The five default keyframes will be added automatically
  4. Adjust their position to control timing
  5. Optionally, modify the Easing curve in the Inspector to customize how the fading in and out feels (e.g. linear, ease-in, smooth)

The Pulse animation options in the Inspector

Here’s an example of what the Pulse animation looks like in action:

Example: the Pulse animation

A Practical Note

Because the Pulse animation relies on the transparency property, be sure that the nodes you apply it to are compatible. Most molecular models in SAMSON support transparency, but always verify that you see an expected result.

Also, don’t forget: you can combine the Pulse effect with other animations to build complex sequences—for example, combining it with the Appear or Flash animations can create attention-grabbing effects step-by-step.

To learn more and explore examples, check out 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 download SAMSON at https://www.samson-connect.net.

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