Make a molecular structure appear, speak, and recede with Pulse

A molecular scene can contain exactly the structures you need—and still be difficult to read. When several models, meshes, or labels are visible at once, viewers may not know where to look. Abruptly showing or hiding objects can also make a presentation feel jumpy. The Pulse animation offers a simple alternative: selected nodes progressively appear, become fully opaque, and then fade away.

This can help when you want to direct attention to one part of a scene without permanently removing other context. For example, you might use a pulse to introduce a structural model, draw attention to a visual model or mesh, or briefly bring a label into view. The animation changes transparency; it does not change the molecular structure itself.

Build the pulse

Start by selecting the nodes you want to animate. Pulse only works on nodes that have a transparency attribute. Structural models, visual models, meshes, and labels are examples of supported node types. If a node does not support transparency, it is not a suitable target for this effect.

With the intended nodes selected, open the Animation panel in the Animator and double-click Pulse. The effect creates five keyframes that describe the full cycle:

  1. Between keyframes 1 and 2, the selected nodes are fully transparent.
  2. Between keyframes 2 and 3, they progressively appear as their transparency decreases.
  3. At keyframe 3, they are fully opaque.
  4. Between keyframes 3 and 4, they progressively disappear as their transparency increases.
  5. Between keyframes 4 and 5, they are fully transparent again.

The central keyframe is the moment of greatest visual emphasis: the selected nodes are opaque there. The fade-in and fade-out intervals give viewers a transition into and out of that moment. Rather than treating the effect as a decorative flourish, think of it as a small visual cue: what should the audience notice while the nodes are most visible?

Shape the timing to fit the explanation

You can move the animation’s keyframes as needed. That lets you adjust when the appearance begins, when the nodes reach full opacity, and when they fade away. For a presentation, consider the order in which you explain the scene: place the fully opaque moment where the relevant structure or label is useful to see, then allow time for the audience to inspect it before the fade-out.

You can also modify the easing curve to change how the parameters are interpolated between frames. This affects the character of the transition between keyframes. It does not change the five-stage sequence, but it gives you control over how the animation progresses from one keyframe to the next.

Example of nodes progressively appearing and disappearing with the Pulse animation

A practical check before presenting

Preview the animation with the same nodes and scene context you plan to use. Confirm that the intended objects are selected, that they support transparency, and that the opaque moment gives viewers a useful view. If the transition feels too fast or too slow for your explanation, move the keyframes. If its progression needs a different feel, adjust the easing curve. These small changes can make a visual sequence easier to follow without adding extra objects or altering the model.

Pulse is one option among related visibility effects, including Appear, Disappear, Show, Hide, and Flash. Choose it when the useful visual story is a gradual entrance, a clear moment of visibility, and a gradual exit.

For the complete instructions, see the Pulse animation documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at www.samson-connect.net.

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