Creating intuitive and visually engaging molecular animations can sometimes feel like a complex task for molecular modelers, especially when working with transparency effects in models. What if there was a tool to make molecular nodes appear and disappear seamlessly? Enter the Pulse animation in SAMSON, a solution for smooth, customizable transparency transitions.
What is the Pulse Animation?
The Pulse animation in SAMSON enables molecular nodes to progressively appear and then disappear. This effect is limited to nodes with transparency attributes, such as structural models, visual models, meshes, and labels. It’s a game-changer for highlighting dynamic molecular structures or labeling transitions in a visually appealing way.
How It Works
The Pulse animation operates through five keyframes to guide the transparency changes. Each keyframe corresponds to a critical stage in the animation:
- Keyframes 1-2: Nodes are fully transparent.
- Keyframes 2-3: Transparency decreases, making nodes progressively visible.
- Keyframe 3: Nodes become fully opaque (no transparency).
- Keyframes 3-4: Transparency increases, making nodes progressively disappear.
- Keyframes 4-5: Nodes return to being fully transparent.
You can adjust the positioning of these keyframes to fine-tune the effect and achieve the desired pacing for your animation.
Adding the Pulse Animation
Setting up the Pulse animation in SAMSON is straightforward:
- Select the nodes that should transition between appearing and disappearing.
- Open the Animation panel within the Animator.
- Double-click the Pulse effect to define the animation.
To further refine the animation, utilize the Easing curve option, which allows you to customize how parameters are interpolated between frames. This provides greater flexibility and precision in tailoring animations to your needs.

Why Use Pulse Animation?
The Pulse animation is particularly useful for molecular modelers aiming to draw attention to specific structural changes or emphasize annotations. Its ability to produce smooth, visually cohesive transitions ensures that your animations remain both professional and informative.
Learn More
The Pulse animation offers a creative way to visualize molecular interactions and communicate your findings effectively. To explore this feature in-depth, visit the official documentation at Pulse Animation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON today at SAMSON Connect.
