A molecular model can contain exactly the information you want to show and still be difficult to read. When several structures, labels, or visual elements compete for attention, viewers may struggle to see which part matters—or miss a transition because an object appears or disappears too abruptly.
The Pulse animation offers a focused way to guide attention: selected nodes progressively become visible, reach full opacity, and then fade away. Rather than changing the molecular data, it animates transparency. That makes it useful when you want to draw attention to a structural model, a visual model, a mesh, or a label while keeping the surrounding presentation intact.
Think of the pulse as a visual cue
Imagine presenting a complex scene and wanting the audience to notice one model or label at a particular moment. A sudden on/off change can feel abrupt. A pulse creates a gradual arrival, a clear moment of full visibility, and a gradual departure. The audience gets time to register the highlighted element, while the rest of the scene can remain available for context.
This is especially helpful when a presentation needs to explain sequence: first establish the scene, then bring attention to a chosen element, and finally let that emphasis recede. The pulse does not explain what a structure means by itself, but it can make the order of a visual explanation easier to follow.
What happens across the five keyframes
The animation uses five keyframes to define a complete appearance-and-disappearance cycle:
- Keyframes 1–2: the selected nodes are fully transparent.
- Keyframes 2–3: they progressively appear as their transparency decreases.
- Keyframe 3: they are fully opaque.
- Keyframes 3–4: they progressively disappear as their transparency increases.
- Keyframes 4–5: they are fully transparent again.
The central keyframe is the moment of maximum visibility. When planning a presentation, consider placing that moment where the audience has enough context to understand why the highlighted object matters. The fade-in and fade-out provide transitions around it; they are not substitutes for choosing a useful moment to emphasize.
Build the animation around your message
Start by selecting the nodes you want to emphasize. Then, in SAMSON’s Animator, double-click Pulse in the Animation panel. The effect is applied to the selected nodes, so it is worth checking the selection before adding the animation. If you intended to highlight a label but selected a structural model as well, both will be part of the animated group.
After adding the effect, move its keyframes as needed. Their placement determines when the stages of the pulse occur in the animation. You can use that flexibility to align the appearance, fully visible moment, and disappearance with the surrounding sequence. The exact timing should serve the explanation: a brief emphasis may suit a quick cue, while a longer visible interval may be easier to follow when the audience needs time to inspect the model.
You can also change how parameters are interpolated between frames by adjusting the easing curve. Easing affects the character of the transition between keyframes. If an element seems to appear or disappear too quickly at part of the transition, the easing curve is one of the settings to review.
Check the target before troubleshooting
Pulse can only be applied to nodes that have a transparency attribute. Structural models, visual models, meshes, and labels are examples of suitable targets. If the effect does not apply to an item as expected, first check whether that node supports transparency rather than assuming the animation or keyframes are at fault.
Used deliberately, a pulse helps solve a familiar presentation problem: making one part of a molecular scene noticeable without removing the context around it. Choose a clear target, place the full-opacity moment where it supports your explanation, and adjust the keyframes and easing to make the transition comfortable to follow.
Learn more in the Pulse animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.