A molecular scene can contain exactly the structures you need and still be difficult to read. When several models, meshes, or labels compete for attention, viewers may not know where to look—or may miss the structure you are trying to introduce. A Pulse animation offers a simple visual cue: selected objects gradually appear, reach full visibility, and then gradually disappear.
This can be useful when preparing an animation or presentation in which you want to draw attention to a particular part of a scene without adding another explanatory label. Instead of making an object visible all at once, the Pulse effect gives its appearance and disappearance a gradual transition.
What the Pulse animation does
Pulse changes the transparency of selected nodes over five keyframes. The sequence begins with the nodes fully transparent. They then progressively appear until they are fully opaque at the middle keyframe. After that, they progressively disappear and end fully transparent.
- 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.
The middle of the sequence is therefore the moment when the selected objects are easiest to see. Consider placing that moment where it best supports your explanation—for example, when you are discussing that object or when the camera view gives it enough visual context. The Pulse effect controls visibility through transparency; it is a presentation aid, not a substitute for choosing a clear view of the molecular scene.
Set it up around your visual goal
First, select the nodes you want to reveal and hide. Pulse can only be applied to nodes that have a transparency attribute. Examples include structural models, visual models, meshes, and labels. If the effect is not applicable to an object, check whether that node supports transparency.
With the nodes selected, open the Animation panel in the Animator and double-click the Pulse animation effect. The animation is added with its five keyframes. You can move the keyframes to adjust when the transition begins, when the object is fully visible, and when it fades away. This makes it possible to align the visual emphasis with the pacing of your presentation.
For example, if viewers need more time to inspect a structure, adjust the keyframe timing so its fully visible portion lasts longer in the animation. If the reveal is only meant as a brief cue, arrange the timing accordingly. The important point is to use the timing to support the explanation, rather than expecting the effect alone to communicate what the object represents.
Use easing to shape the transition
The timing of keyframes determines where the stages occur. The Easing curve determines how parameter values are interpolated between frames, and can be changed in the animation properties. If the transparency transition feels too abrupt or too gradual for your scene, adjusting the easing curve is another way to refine how it progresses. Preview the result and choose the transition that makes the object easiest to follow.
Pulse is most helpful when used with intention: choose a clear subject, give viewers time to recognize it, and make sure the visual emphasis fits the surrounding scene. For details on adding the animation and editing its properties, see the Pulse animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.