In molecular modeling, one persistent challenge is effectively conveying how structures transiently appear and disappear during processes like docking, folding, or dynamic transformations. Researchers often want to emphasize certain regions of a molecular system momentarily — perhaps to draw attention to a transient binding site, or simply to produce cleaner visual explanations for presentations or educational content.
If you’ve ever tried dimming parts of a molecular model to fade them in and out … only to end up fiddling with transparency frames that don’t align well, you’re not alone. Fortunately, there’s a built-in solution in SAMSON: the Pulse animation effect.
The Pulse Effect at a Glance
The Pulse animation makes selected nodes — such as structural models, visual models, meshes, and labels — gradually appear, become fully visible, and then fade out. It works specifically on nodes that support transparency, making this technique particularly useful when you want soft transitions rather than abrupt visibility toggles.
Here’s an illustration of what to expect:
Why Use Pulse Animation?
The Pulse effect is incredibly useful when trying to:
- Highlight transient structures without cluttering the scene
- Animate ligand binding/unbinding processes intuitively
- Fade in key annotation labels exactly when needed
- Create more engaging presentations or teaching materials
Instead of manually scripting these transitions or stacking multiple visibility animations, Pulse provides a predefined keyframe logic:
- Keyframes 1-2: Fully transparent
- Keyframes 2-3: Gradually becomes visible
- Keyframe 3: Fully opaque
- Keyframes 3-4: Gradually disappears
- Keyframes 4-5: Fully transparent again
This makes it easy to represent short-lived molecular components with clarity, reducing visual overload while guiding the viewer’s focus.
How to Apply Pulse Animation in SAMSON
- Select the nodes you wish to animate. These must be capable of transparency — most standard models and labels are.
- Open the Animator, and double-click on the Pulse option in the Animation panel.
- Adjust the timing by dragging keyframes directly on the timeline.
- Optionally, fine-tune the tempo of the transition using the Easing curve in the Inspector panel.
Here’s what the animation settings look like:
Tips for Using Pulse Effectively
If you’re using the Pulse animation to model a chemical mechanism, consider syncing Pulse transitions with color changes or structural deformations for even more expressive animations. You can insert additional keyframes or combine Pulse with other visibility effects such as Flash or Appear to create layered storytelling.
By keeping your animations simple and focusing the viewer’s attention, Pulse can reduce the cognitive load and help others better understand spatial and temporal aspects of your molecular scenes.
To learn more and see complete instructions, visit the full documentation for Pulse animation at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.