In molecular modeling, clear visual storytelling is often just as important as the molecular data itself—especially when communicating findings or creating educational material. A common challenge modelers face is how to effectively highlight specific molecular structures or dynamics in a clear yet dynamic way. This is where Pulsing animations can offer subtle, rhythmic cues that draw a viewer’s attention without abrupt transitions.
If you’re working in SAMSON, the integrative molecular design platform, you might want to make certain structures subtly appear and disappear—perhaps to emphasize surface features or to rhythmically highlight important areas like active sites, ions, or structural motifs. The Pulse animation does exactly that, providing a looping fade-in/fade-out effect that can be a visual anchor point for your viewers. Here’s how it works and how to integrate it into your next molecular presentation.
What is Pulse Animation?
The Pulse animation in SAMSON smoothly transitions molecular nodes—such as structural models, visual models, meshes, and even labels—from transparent to opaque, and then back again. It leverages the transparency attribute, so ensure your nodes support it before applying the effect.
Why Use It?
If you’ve ever tried to emphasize something in a molecular scene using static color changes or static visibility toggles, you know they can be abrupt or easy to miss. The Pulse animation offers a more rhythmic, eye-catching solution that draws attention without distracting, ideal for highlighting key regions in a looped visualization, showcasing periodic behavior, or simply improving the flow of a presentation.
Adding the Pulse Animation
1. Select the nodes you want pulsed—these should support the transparency property.
2. Open the Animation panel within the Animator section.
3. Double-click on Pulse to apply it to the selected elements.
Understanding the Animation Timeline
The Pulse animation is composed of five keyframes:
- Keyframe 1 to 2: Nodes are fully transparent.
- Keyframe 2 to 3: Transparency decreases—nodes appear.
- Keyframe 3: Nodes are fully visible.
- Keyframe 3 to 4: Transparency increases—nodes disappear again.
- Keyframe 4 to 5: Nodes return to full transparency.
You can freely shift these keyframes along the timeline to control the speed and rhythm of the pulse.
Fine-Tuning with Easing Curves
Sometimes a linear transition might feel too mechanical. To create more organic or cinematic effects, you can adjust how the animation interpolates between keyframes using the Easing curve control in the animation’s Inspector panel.
Where It Fits Best
The Pulse animation is particularly useful in presentations, tutorials, or educational videos where you want parts of your model to draw subtle attention without overwhelming the rest of the scene. By creating a repeating visual pulse, you can keep the viewer engaged while reinforcing structure recognition or functional significance.
To learn more and try the animation for yourself, visit the original documentation page: 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