Visualizing complex molecular systems can be overwhelming, especially when trying to guide your audience’s attention or highlight dynamic elements in your presentation. Whether you’re preparing a research talk, teaching a class, or sharing insights with colleagues, animations can help make your molecular models more comprehensible.
One common challenge is how to make molecular components fade in and out smoothly, in a way that feels natural and helps showcase transitions or interactions without sudden visual disruptions. This is where the Pulse animation in SAMSON comes in handy.
The Pulse animation offers a simple yet effective way to make nodes (such as structural models, visual models, meshes, or labels) appear and disappear gradually by adjusting their transparency. This is particularly useful for:
- Teaching molecular dynamics: Focus attention on fluctuating regions of a molecule
- Guiding presentations: Emphasize specific domains before transitioning to others
- Comparing model states: Fade between conformations naturally
How the Pulse Effect Works
The Pulse animation uses five keyframes to control transparency:
- Keyframes 1 → 2: Nodes stay fully transparent
- Keyframes 2 → 3: Nodes appear by decreasing transparency
- Keyframe 3: Nodes are fully opaque
- Keyframes 3 → 4: Nodes disappear by increasing transparency
- Keyframes 4 → 5: Nodes return to fully transparent
This gives your model a breathing or pulsing effect—hence the name.
Getting Started
To apply the Pulse animation in SAMSON:
- Select the nodes you’d like to animate. These must support transparency, such as structural models or labels.
- Open the Animation panel of the Animator.
- Double-click on the Pulse effect to apply it.
You can drag the keyframes along the timeline to control how long each phase lasts, offering flexibility to match your pacing and visual storytelling.
Customizing the Pulse
Through the Inspector, you can adjust the transition behavior of the animation. By changing the Easing curve, you control whether the transparency change feels linear, abrupt, or smooth.
For example, a quadratic ease-in can make the appearance feel more gradual, ideal for focusing attention subtly. Try experimenting with these options to match the tempo and mood of your presentation.
Visual Example
Here, transparent nodes pulse into full visibility and fade out again, drawing attention without overwhelming the viewer.
Conclusion
The Pulse animation provides a simple yet effective method for highlighting components of your molecular model in a non-disruptive way. Whether you’re preparing teaching materials or aiming to communicate complex processes clearly, Pulse adds clarity and motion in a controlled fashion.
To learn more, visit the documentation page here: 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.