Reveal a molecular model in stages—without changing its transparency

A molecular model can become difficult to explain when every component is visible at once. A crowded view may hide the feature you want people to notice, while repeatedly switching nodes on and off during a presentation can interrupt the story. The Shown animation offers a way to plan those visibility changes along an animation timeline.

Its key distinction is easy to miss: Shown changes node visibility, not transparency. In other words, it is for making selected nodes shown between keyframes, rather than gradually making them more or less see-through. That matters when you want a clean reveal—for example, introducing a molecular component at a particular point in an explanation without suggesting that the component itself is fading or changing material properties.

Plan the reveal before adding it

Start with the audience’s question: what should they be looking at first, and what should appear next? A useful sequence might establish the overall model, then reveal a selected set of nodes that supports the next point. You do not need to animate everything. Keeping the reveal focused can make a complex scene easier to follow.

Before adding the effect, choose the nodes you want to show. This selection step is important: the animation acts on the chosen nodes, so check that your selection matches the intended reveal. If the wrong parts appear, review the selected nodes before adjusting the timeline.

Add Shown to the timeline

1. Select the nodes that should be shown.
2. Open the Animation panel in the Animator.
3. Double-click the Shown animation effect. Its begin keyframe is set at the current frame.
4. Move the animation’s keyframes as needed to place the effect in your sequence.

The practical takeaway is that the current frame matters when you create the effect: it determines where the begin keyframe is initially placed. If the reveal belongs later in your presentation, you can move the keyframes rather than starting over. Check the result in context with the rest of the timeline, especially if you are building several steps in sequence.

Choose the right kind of effect

Use Shown when the goal is to have nodes shown between keyframes. If your intended effect is about transparency rather than visibility, Shown is not the same thing. SAMSON also documents related animation effects such as Appear, Disappear, Show, and Hide. Choosing an effect based on the visual change you actually want helps avoid a reveal that communicates the wrong thing.

You can also adjust how parameters are interpolated between frames by changing the Easing curve. When refining an animation, review the transition in the context of the full presentation and make sure the timing supports the point you are explaining. The documentation notes that keyframes can always be moved, so timing can be revised as your sequence takes shape.

For a more legible molecular presentation, treat visibility as part of the explanation: select the relevant nodes, place the reveal where it supports your narrative, and use Shown when you need a visibility change rather than a transparency change.

Learn more about the Shown animation in the SAMSON documentation.

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