A molecular scene can become difficult to read when every structure, label, and visual element remains visible at once. Hiding an object can clear space quickly, but an abrupt change may make it harder for viewers to follow what changed. The Disappear animation offers a gradual alternative: selected nodes become increasingly transparent over time.
This is useful when you want to shift attention between parts of a molecular model—for example, fading a visual element out of the way while keeping the rest of the scene visible. The transition can make the change in emphasis easier to follow than an immediate hide, while still letting you decide when the element is fully gone.
Choose the right node
Before adding the animation, select the node or nodes you want to fade. Disappear works progressively on nodes that have a transparency attribute, including structural models, visual models, meshes, and labels. For nodes without that attribute, it behaves similarly to the Hide animation instead.
There is an important detail when working with atoms and bonds: individual atoms and bonds do not have their own opacity attribute. Their structural models do. If your goal is to change the transparency of atoms or bonds, apply Disappear to the relevant structural model, rather than selecting individual atoms or bonds and expecting them to fade independently.
Build the fade in the Animator
- Select the nodes you want to affect.
- In the Animator, open the Animation panel and double-click Disappear.
- Review the animation’s four keyframes and move them to suit the timing of your presentation.
The keyframes define three parts of the effect. Between the first and second, the selected nodes remain fully opaque. Between the second and third, they progressively become more transparent. Between the third and fourth, they remain fully transparent. In practice, the middle section is the visible fade: placing its keyframes farther apart gives the transition more time, while bringing them closer together makes it happen over a shorter interval.
That timing lets you coordinate a fade with the pace of your explanation. You might keep a structure visible while introducing it, fade it during a transition to another feature, and leave it transparent once it is no longer needed. The keyframes can be moved whenever you need to revise the sequence; you do not have to treat their initial positions as fixed.
Make the transition fit the scene
The animation’s Easing curve controls how its parameters are interpolated between frames. If the fade feels too abrupt at some point or too gradual at another, adjusting the curve can change the character of the transition without changing which nodes are selected. Preview the result in the context of the whole scene: a fade that works for one model may be hard to notice if the surrounding elements are also changing.
One useful planning check is to ask what the audience should still be able to see at each moment. Keep the relevant structure fully visible for as long as it is being discussed, use the transparency interval to guide attention elsewhere, and decide whether the fully transparent end state should persist through the next part of the presentation. This makes the animation serve the explanation rather than simply adding motion.
To explore the animation and its settings, see the Disappear documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.