Molecular modeling often involves communicating complex structural changes or emphasizing specific features of a model. But making molecules “pop” visually in presentations or animations can be tricky, especially when you want a dynamic and engaging representation that stays scientifically accurate. If you’ve ever needed a neat way to highlight components in your scenes — without overwhelming your audience — SAMSON’s Pulse animation could be what you’re looking for.
Pulse is a subtle but effective looping effect that smoothly makes molecular nodes appear and disappear in a rhythmic pattern. It helps keep casual viewers engaged while maintaining focus on selected regions of interest. This animation is particularly suitable when you need to:
- Draw attention sequentially to different parts of a model
- Create a breathing visual effect, akin to a heartbeat
- Animate transitions during a presentation without abrupt changes
What Pulse Does
The Pulse animation works by varying the transparency of selected nodes. This could include structural models, visual models, meshes, or labels. By applying Pulse, these elements gradually fade in and out — a kind of visual “breathing” that can make your animation smoother and more engaging without being distracting.
It’s especially helpful when showcasing molecular interactions: instead of toggling elements on and off abruptly, Pulse offers an elegant way to keep viewers oriented while changing focus.
How the Animation Works
To apply the Pulse effect:
- Select the molecules or labels you want to animate.
- Open the Animation panel in the Animator.
- Double-click Pulse to apply it to your selection.
Pulse is composed of 5 keyframes, each controlling a phase in visibility:
- Keyframe 1-2: Fully transparent
- Keyframe 2-3: Gradually appears
- Keyframe 3: Fully opaque
- Keyframe 3-4: Gradually fades away
- Keyframe 4-5: Fully transparent again
The keyframes can be adjusted in time for faster or slower effects. The transition between these frames may be further refined using easing curves to specify how smooth or sharp the transparency changes are.
Inspecting and Adjusting Parameters
Once the animation is applied, you can use the Inspector to adjust timing and interpolation. This gives precise control over the visual rhythm of molecules fading in and out — making it easy to match the beat of a narration or background audio if you’re preparing a video or live seminar.
Visual Example
Below is a short animation showing the Pulse effect applied to a molecular scene. Notice the smooth transparency transitions and how it keeps visual interest around the nodes:
This looping effect can also be paired with other animations like Flash or Show to create layered effects, increasing clarity when needed without overwhelming the viewer.
Learn more about how to apply and customize the Pulse animation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.