Make a molecular structure pulse into view—without losing the audience

A molecular scene can contain the detail you need and still be difficult to follow. When a structure, label, or other visual element appears all at once, viewers may not know where to look. A pulse animation offers a simple way to draw attention: the selected nodes gradually appear, reach full visibility, and then gradually disappear.

This can be useful when preparing an animation or presentation in which a component should be noticed temporarily rather than remain visible throughout. The key is to treat the pulse as a visual cue: decide what the audience should notice, apply the animation to those nodes, and adjust its timing to fit the surrounding sequence.

Start with nodes that support transparency

Pulse works only on nodes with a transparency attribute. Examples include structural models, visual models, meshes, and labels. If an element cannot be made transparent, this is not the appropriate animation for it. Checking the type of node first can save time when an animation seems to have no visible effect.

Choose the nodes you want to progressively show and hide. Then, in the Animator, double-click Pulse in the Animation panel. The animation is added to the selected nodes, and you can move its keyframes to position the effect in your sequence.

Read the five-keyframe rhythm

Pulse uses five keyframes to create a complete appearance-and-disappearance cycle:

  1. Keyframes 1–2: the nodes are fully transparent.
  2. Keyframes 2–3: they progressively appear as their transparency decreases.
  3. Keyframe 3: they are fully opaque.
  4. Keyframes 3–4: they progressively disappear as their transparency increases.
  5. Keyframes 4–5: they are fully transparent again.

Thinking of the animation as a rhythm helps when arranging it. The middle keyframe is the moment of full visibility; the intervals on either side control the gradual reveal and fade. Moving the keyframes changes where those moments fall in the animation. For example, you can reposition the cycle so its fully visible moment lines up with the part of your presentation where the structure matters most. You can also move keyframes whenever you need to refine the timing.

Example of nodes progressively appearing and disappearing with the Pulse animation
The five-keyframe Pulse cycle, from transparent to visible and back.

Use easing to shape the transition

The keyframes define the stages of the effect, while the easing curve changes how parameters are interpolated between frames. Adjusting the easing curve gives you a way to modify the character of the transitions without changing the basic five-stage sequence. If the reveal or fade does not feel right in context, inspect the easing options and review the result in the animation.

Pulse animation options in the Inspector
Pulse animation options in the Inspector.

A quick planning check

Before using Pulse, ask three questions: Is the selected node transparent-capable? Is a temporary reveal more helpful than leaving the element continuously visible? And does the fully visible moment occur when the viewer needs to see the element? These checks keep the effect purposeful and help prevent a pulse from becoming a distraction.

For the exact setup steps and animation details, see the Pulse animation documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.

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