A molecular scene can contain exactly the structures you need and still be difficult to read. When a component is no longer relevant, hiding it immediately may make the presentation feel abrupt; leaving it visible can distract from the detail you want people to notice. The Disappear animation offers a gradual transition: selected nodes become increasingly transparent, helping viewers follow a change in focus.
This is especially useful when presenting a complex model in stages. You might want to draw attention to one part of a scene, then let another set of nodes recede from view. A fade can make that change easier to follow than a sudden switch, while keeping the presentation focused on the information that matters at that moment.
What the animation changes
Disappear progressively increases the transparency of nodes that support a transparency attribute. The documentation gives structural models, visual models, meshes, and labels as examples. Nodes without a transparency attribute are treated more like they are in the Hide animation: they disappear by being hidden rather than by fading through transparency.
One important detail for molecular scenes: individual atoms and bonds do not have an opacity attribute. Their structural models do. So if your goal is to fade atoms and bonds, apply Disappear to the relevant structural model, not to individual atoms or bonds. Keeping this distinction in mind can save time when an animation does not produce the gradual effect you expected.
Set up a controlled fade
- Choose the nodes. Identify the scene elements you want to fade. Be deliberate: selecting a structural model affects its atoms and bonds visually, while selecting a label or mesh targets that node.
- Add Disappear. In the Animator, open the Animation panel and double-click the Disappear animation effect.
- Check the four keyframes. Between keyframes 1 and 2, the selected nodes are fully opaque. Between 2 and 3, their transparency increases progressively. Between 3 and 4, they are fully transparent.
- Adjust the timing. Move the keyframes to control when the fade begins and ends in your presentation. You can also modify the easing curve to change how the animation parameters are interpolated between frames.
A practical way to refine the result is to play the animation and watch specifically for two things: whether the fade starts at the right moment, and whether its duration gives the viewer enough time to register what is changing. If the transition feels rushed or lingers too long, reposition the keyframes. This is a presentation choice rather than a change to the molecular structure itself.
When a fade is not the right effect
If you need an element to vanish without a transparency transition—or if the node does not support transparency—Disappear behaves similarly to Hide. If you want to bring an element back into view, see the related Appear animation. For other presentation effects, the documentation also lists Flash, Pulse, Show, and Hidden.
For the full instructions and animation details, visit the Disappear animation documentation.
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