A molecular model can contain exactly the structure you want to explain and still be difficult to present. When every component remains equally visible, it may be hard for viewers to follow a change or focus on the part that matters. Making selected parts progressively disappear can help create a clearer visual transition—provided you apply the effect to the right nodes.
In SAMSON, the Disappear animation gradually increases the transparency of selected nodes. It is useful when you want a model, mesh, or label to fade from view rather than vanish all at once. The important detail is that the animation works on nodes that have a transparency attribute. Structural models and visual models are examples of nodes that can have one.
Choose the object that controls visibility
Atoms and bonds do not have their own opacity attribute. Their structural models do. So if your goal is to change the transparency of atoms and bonds, select and animate the relevant structural model, rather than trying to apply the effect to individual atoms or bonds. This distinction can save time when an animation appears not to affect the elements you expected.
Before adding the effect, decide what should remain visible while the selected part fades. For example, you might want a structural model to recede while a label stays on screen, or fade a mesh while keeping the surrounding model visible. Selecting only the intended nodes gives the transition a clear purpose and helps avoid fading more of the scene than you meant to.
Build the fade in the Animator
First, select the nodes you want to progressively disappear. Then, in the Animator, open the Animation panel and double-click the Disappear effect. The animation contains four keyframes, with three useful phases:
- Keyframes 1–2: the selected nodes are fully opaque.
- Keyframes 2–3: the nodes progressively become more transparent.
- Keyframes 3–4: the nodes are fully transparent.
This structure gives you time to establish the original view, show the fade, and then hold on the result. Move the keyframes to adjust where those phases fall in your presentation. If the disappearance feels rushed, give the transition more room; if it distracts from the next point, shorten it. The keyframes are movable, so you can tune the sequence to suit the pace of your explanation.
Use the easing curve to shape the transition
The keyframes determine the animation’s phases, while the easing curve controls how parameters are interpolated between frames. If the change does not feel right, adjusting the easing curve is another option, alongside moving the keyframes. These controls let you refine the transition without changing the basic idea: the selected nodes start visible, fade, and end transparent.
One practical check is to play through the animation and ask whether the viewer can still understand the scene during the fade. Keep the context needed for the explanation visible, and make sure the disappearing object is the one you intended to target. For nodes without a transparency attribute, Disappear behaves similarly to the Hide animation, so the gradual transparency effect is specifically tied to nodes that support transparency.
Use Disappear when a gradual visual handoff is more useful than an abrupt change. For details on adding the animation and its properties, see the SAMSON Disappear animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.