When building compelling molecular presentations or demonstrating mechanisms in your chemical or biological models, static visuals often fall short in conveying dynamic behavior. Were you ever in a situation where highlighting part of your model felt like not enough—where you wished you could guide your audience’s attention more effectively? If so, the Pulse animation in SAMSON might be just what you need.
The Pulse animation effect allows modelers to make specific components of a molecular system progressively appear and disappear, providing an elegant way to focus attention, enhance clarity, or introduce visual rhythm into a scientific animation. This is especially useful when you want to emphasize certain nodes—like molecular surfaces, labels, or structural components—without overwhelming viewers with a constant visual presence.
What is the Pulse animation?
The Pulse animation is designed for nodes that support transparency, such as:
- Structural models
- Visual models
- Meshes
- Labels
The animation works by adjusting the transparency of the selected elements in a five-keyframe sequence. These keyframes define how nodes phase in from full transparency to full opacity and then fade back out. The result is a smooth visual rhythm that resembles a “pulse.”
How it works
Here’s how the 5 keyframes are structured:
- Keyframes 1 to 2: Nodes remain fully transparent.
- Keyframes 2 to 3: Transparency decreases—nodes begin to appear.
- Keyframe 3: Nodes are fully opaque—highlighted and visible.
- Keyframes 3 to 4: Transparency increases—nodes begin to disappear.
- Keyframes 4 to 5: Nodes return to being fully transparent.
You have full control over the timing—keyframes can be moved to speed up or slow down the effect. The easing curve can also be adjusted to customize how the transparency transition interpolates over time. This makes it easy to integrate the Pulse animation seamlessly into longer sequences, especially when paired with other animation types like Appear or Flash.
Applying the Pulse effect
To add the Pulse animation to your model:
- Select the nodes you’d like to animate—these must support transparency.
- Open the Animation panel in the Animator.
- Double-click on the Pulse animation effect.
- Adjust keyframes and easing curves to fit your animation timeline.
This effect is particularly helpful in scenarios where you want to draw attention to specific features temporarily—like binding sites, ligand regions, or subunits—without cluttering the entire animation with permanent visuals.
Visual example
Below is an example of what the Pulse animation looks like in practice:
Final thoughts
The Pulse animation in SAMSON gives molecular modelers a subtle yet effective tool to enhance clarity and focus in visual presentations. If you’re working on instructional materials, scientific communication, or publications involving molecular simulations, consider experimenting with this animation style. It’s straightforward to implement and helps guide viewer attention in a dynamic way.
To learn more about setup and options, visit the original SAMSON documentation page: https://documentation.samson-connect.net/users/latest/animations/pulse/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.