A molecular scene can contain exactly the information you need and still be hard to read. When several models, meshes, or labels compete for attention, hiding an object outright may make the transition feel abrupt: the viewer sees the scene change, but not what is being de-emphasized. A gradual disappearance offers another option. It lets you guide attention by changing transparency over time.
In SAMSON, the Disappear animation progressively makes selected nodes transparent when those nodes have a transparency attribute. That includes structural and visual models, meshes, and labels. It can be useful when you want to reduce visual clutter during a presentation—for example, by fading a model or label out as the explanation moves to another part of the scene.
Set up the fade
- Select the nodes you want to fade. Think about the audience’s current question: which visual elements are no longer needed to answer it?
- In the Animator, open the Animation panel and double-click Disappear.
- Review the animation’s four keyframes, then move them as needed to fit the timing of your presentation.
The keyframes define the basic progression: between frames 1 and 2, the selected nodes remain fully opaque; between frames 2 and 3, they progressively become transparent; and between frames 3 and 4, they remain fully transparent. In other words, the fade happens in the middle portion of the animation, with opaque and transparent portions on either side.
This structure gives you a useful way to plan the transition. If viewers need time to inspect the initial scene, allow enough time before the fade begins. If they need to follow the change itself, give the transition room rather than rushing through the middle keyframes. The documentation notes that the keyframes can be moved, so you can adjust the animation’s timing to suit the sequence you are presenting.
Choose the right level of the scene
One important detail: individual atoms and bonds do not have an opacity attribute. Their structural models do. If your goal is to change the transparency of atoms and bonds, apply Disappear to the relevant structural model, rather than to individual atoms or bonds. Applying the animation to a node without a transparency attribute produces behavior similar to the Hide animation, so the result may be an abrupt change instead of a gradual fade.
This distinction can save time when an animation does not look as expected. Before adjusting the timing, check what you selected and whether that node supports transparency. The intended target and the animation’s timing are separate parts of the setup: the right keyframes cannot create a gradual transparency change on a node that does not have the needed attribute.
Shape the transition
You can change how parameter values are interpolated between frames by modifying the easing curve. This affects the character of the transition: it determines how the change progresses between keyframes. If the fade feels too sudden or too gradual, the easing curve is one setting to review, alongside the placement of the keyframes. The best choice depends on the pace and purpose of the presentation; the goal is simply to make the visual change easy to follow.
Quick check: select the model or other node you mean to fade, confirm it has a transparency attribute, add Disappear from the Animator’s Animation panel, then adjust the keyframes and easing curve. This separates three common questions—what is fading, when it fades, and how the change progresses—and makes troubleshooting more straightforward.
For the full instructions, visit the Disappear animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.