Breathing Life Into Molecular Models With Pulse Animation

Creating compelling molecular animations can be challenging, especially when your goal is to capture attention or communicate a dynamic process effectively. Perhaps you’ve built a beautiful molecular assembly, set up the perfect camera angle, and composed the ideal scene—but something about it still feels static. If you’ve ever faced this, you’re not alone.

Molecular modeling is not just about precision—it’s also about presentation. Whether you’re building a trailer for a scientific publication, an educational video, or simply want to highlight part of your simulation results, giving your model a temporal rhythm can make all the difference. That’s where the Pulse animation in SAMSON comes in handy.

What is the Pulse Animation?

The Pulse animation is an effect that smoothly cycles a node’s transparency level—progressively making it appear and then disappear. This works particularly well for structures where transparency is already meaningful, such as structural models, visual models, meshes, and labels. Essentially, it helps your selection of nodes breathe in and out on-screen.

Why Use Pulse?

Pulse animations add subtle attention-focus to your model. For example:

  • Want to emphasize a ligand entering an active site? Pulse it.
  • Want viewers to notice a key protein domain? Pulse it.
  • Want to loop through visual layers for teaching purposes? Pulse transparency in and out.

Because the opacity progresses gradually, the animation avoids sudden appearing/disappearing effects, resulting in a rhythm both informative and visually soothing.

Adding the Pulse Animation

Here’s how to apply this animation:

  1. Select the nodes you want to show and hide progressively.
  2. Double-click on the Pulse animation in the Animation panel inside the Animator.
  3. The animation adds 5 keyframes:
    • Between keyframes 1 and 2: fully transparent
    • Between keyframes 2 and 3: gradually becomes opaque
    • Keyframe 3: fully opaque
    • Between keyframes 3 and 4: gradually becomes transparent
    • Between keyframes 4 and 5: fully transparent again
  4. Move the keyframes as necessary to control timing—for example, lengthen the pause at full opacity to highlight an important part.

Pulse animation example

Tuning the Animation

Like most SAMSON animations, Pulse can be tuned further for a natural feel. Use the Easing curve in the animation’s Inspector panel to control how quickly the transparency changes happen between keyframes. For instance, easing-out curves can slow the fade-out effect for a more graceful disappearing act.

Pulse animation in the Inspector

Useful Tips

  • If you only apply Pulse to a few nodes alongside static components, it can act as a visual guide, leading the viewer’s eye.
  • Use Pulse at different durations and at multiple times in the timeline to create asynchronous transparency cycles across components.
  • Pair Pulse with color transitions for added visual differentiation (e.g., during conformational transitions).

Animations don’t need to be flashy to stand out. Sometimes, just a gentle transparency rhythm is enough to draw interest while maintaining scientific clarity.

To learn more, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/pulse/

SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.

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