A molecular structure can contain exactly the detail you need—and still be difficult to present. When a region suddenly vanishes, viewers may lose track of what changed or where to look next. A gradual fade offers a simple alternative: it lets you shift attention away from selected parts of a model while keeping the transition visible.
In SAMSON, the Disappear animation progressively makes selected nodes transparent. This can help when preparing a molecular presentation, explaining a structural change, or reducing visual clutter in a sequence. Instead of an abrupt switch from visible to hidden, the fade gives your audience a moment to follow the change.
Apply the fade to the right node
Start by choosing the nodes you want to disappear. Then, in the Animator, open the Animation panel and double-click the Disappear effect. The choice of node matters: the animation changes transparency only for nodes that have a transparency attribute, such as structural models, visual models, meshes, and labels.
A common source of confusion is selecting individual atoms or bonds. They do not have their own opacity attribute; their structural models do. So, if the goal is to fade atoms and bonds, apply the animation to the relevant structural model rather than to the individual atoms or bonds. For nodes without a transparency attribute, Disappear behaves similarly to the Hide animation, rather than producing a gradual fade.
Use the four keyframes to shape the transition
Disappear has four keyframes, giving the effect a clear progression:
- Keyframes 1–2: the selected nodes remain fully opaque.
- Keyframes 2–3: their transparency increases, so they progressively disappear.
- Keyframes 3–4: they remain fully transparent.
This structure is useful because the fade is not the entire animation. The opening interval keeps the model visible before the transition begins, and the final interval holds the transparent state after it ends. Move the keyframes to adjust where those stages fall in your presentation. For example, you can give viewers more time to inspect the original structure before the fade, or leave a longer interval after it so attention can settle on what remains.
Make the fade serve the explanation
Before adding the effect, decide what the audience should notice. If a component is about to become less relevant, fading it can make the next point easier to see without changing the underlying molecular explanation. If viewers need to compare the complete structure with the reduced view, leave time for both states to register. Keep the transition focused on the nodes that support that story; fading too much at once can make it harder to understand what the remaining model represents.
You can also change how parameters are interpolated between frames by modifying the animation’s easing curve. This controls the interpolation between keyframes, while moving the keyframes controls when the stages occur. These are separate ways to adjust the motion: use timing to place the fade in your sequence, and easing to change how the transition progresses between frames.
One practical check before presenting: confirm that you applied the effect to the intended model or other transparency-capable node, then review the keyframe positions and the resulting transition. If the target simply switches off instead of fading, check whether the selected node has a transparency attribute and, for atoms or bonds, try the structural model.
For the complete instructions, see the SAMSON Disappear animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.