A molecular model can contain exactly the structures you need and still be difficult to present clearly. When several models, meshes, or labels are visible at once, viewers may struggle to tell what matters—or when a particular part becomes relevant. The Pulse animation offers a simple visual cue: selected nodes progressively appear, remain visible briefly, and then progressively disappear.
This can help when building an animation that introduces a structure and then clears the view for the next part of a presentation. Rather than switching abruptly between visible and invisible, Pulse changes transparency over time, giving the viewer a gradual transition to follow.
Choose suitable nodes first
Pulse can only be applied to nodes that have a transparency attribute. Examples include structural models, visual models, meshes, and labels. Before adding the animation, select the nodes you want to bring into view and later fade out. This selection is important: the effect applies to the chosen nodes, so it is worth checking that the selection matches the visual element you intend to emphasize.
Once the nodes are selected, double-click Pulse in the Animation panel of the Animator. The animation is built from five keyframes. Together, they describe a complete cycle from transparent, to visible, and back to transparent:
- Keyframes 1–2: the selected nodes are fully transparent.
- Keyframes 2–3: they progressively appear as their transparency decreases.
- At keyframe 3: they are fully opaque, with no transparency.
- Keyframes 3–4: they progressively disappear as their transparency increases.
- Keyframes 4–5: they are fully transparent again.
This sequence is useful for planning the timing of a visual explanation. For example, you might position the fully opaque point at the moment you want the audience to focus on the selected structure, then adjust the surrounding keyframes to control when the fade-in and fade-out occur. You can move the animation’s keyframes as needed, so the transition can be fitted to the timing of the rest of your animation.
Use the fade to guide attention
A gradual appearance is most helpful when it supports a clear sequence. Consider what the viewer should notice before the selected nodes appear, while they are fully visible, and after they disappear. If the fade overlaps with other visual changes, the audience may have more than one thing to interpret at once. Adjusting the keyframe positions gives you a way to refine that sequence without changing which nodes the animation targets.
The transition’s character can also be adjusted. Pulse lets you change how its parameters are interpolated between frames using the easing curve. In practical terms, this gives you control over how the change progresses between keyframes. If the default transition does not suit the pacing of your presentation, the easing curve is the relevant property to explore.
For a useful first test, apply Pulse to one appropriate node or a small group, inspect the full five-keyframe sequence, and adjust the keyframe positions to fit your intended timing. Then consider whether the change in transparency makes the structure easier to follow. A deliberate fade can make an otherwise abrupt transition easier to read, while keeping the underlying molecular scene unchanged.
For the complete instructions and property details, see the Pulse animation documentation.
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