A molecular scene can contain more detail than a viewer can absorb at once. Showing every component throughout an explanation may create visual clutter; switching abruptly between views can make it difficult to see what the audience should notice. A gentle change in transparency offers another option: bring a selected part of the scene into view, hold attention on it, then let it fade away.
In SAMSON, the Pulse animation does this by progressively revealing and hiding selected nodes. It can be useful when you want to direct attention to a structural model, a visual model, a mesh, or a label without suggesting that the object has moved or changed its molecular structure. Pulse changes visibility through transparency; it is not a motion animation.
Build a reveal-and-fade sequence
Start by choosing the nodes you want to emphasize. Then, in the Animator’s Animation panel, double-click the Pulse effect. The animation contains five keyframes that define a complete cycle:
- Between keyframes 1 and 2, the selected nodes are fully transparent.
- Between keyframes 2 and 3, they progressively appear as their transparency decreases.
- At keyframe 3, they are fully opaque.
- Between keyframes 3 and 4, they progressively disappear as their transparency increases.
- Between keyframes 4 and 5, they are fully transparent again.
This sequence gives you a natural visual rhythm: begin with the detail out of view, reveal it, give the audience a moment to inspect it, and then clear the scene again. For example, you could use a pulse to draw attention to a label or mesh while keeping other selected scene elements from competing for attention. The animation does not decide what matters; your node selection determines what receives the emphasis.
Adjust the timing to suit the explanation
The default keyframe arrangement is a starting point, not a fixed schedule. Move the keyframes to change how the sequence fits your presentation. If viewers need more time to examine the fully visible detail, adjust the timing so that the opaque part of the pulse lasts longer. If the reveal feels rushed or too slow, reposition the relevant keyframes and review the result.
You can also change how the animation’s parameters are interpolated between frames by modifying its easing curve. Easing affects the character of the transitions between keyframes; it gives you a way to refine how the appearance and disappearance progress, rather than changing which nodes are animated. The Inspector shows the Pulse animation options.
Check compatibility before applying it
Pulse requires nodes to have a transparency attribute. It can be applied to supported items such as structural models, visual models, meshes, and labels. If a chosen node does not support transparency, Pulse is not the appropriate effect for it. When planning a sequence, also consider whether fading the selected object communicates your intent clearly: a fade can focus attention, but it can also be mistaken for an object being removed from the scene. Keeping the reveal and fade tied to a clear explanatory point helps viewers understand why the detail changes visibility.
For a concise way to manage visual emphasis, think of Pulse as a spotlight made from transparency: select the nodes, place the reveal where the audience needs it, and adjust the keyframes and easing to make the timing comfortable to follow.
Learn more in the Pulse animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.