A molecular scene can contain exactly the structures you want to show and still be difficult to follow. If every component is visible at once, viewers may not know where to look; if a structure suddenly pops into view, the change can distract from the explanation. A gradual reveal offers a simple way to guide attention: keep a selected node hidden at first, then let it appear over time.
In SAMSON, the Appear animation progressively reveals eligible nodes by changing their transparency. It can be useful when building a presentation in which a model, mesh, visual model, or label should enter the scene at a particular moment rather than being visible from the beginning.
Start with the right node
Before adding the effect, select the node or nodes you want to reveal. The key detail is that Appear works with nodes that have a transparency attribute. Structural models, visual models, meshes, and labels are examples of nodes that can use this kind of gradual change.
Atoms and bonds themselves do not have an opacity attribute. Their structural models do. So, if the goal is to fade in atoms and bonds, apply the animation to the relevant structural model, not to the individual atoms or bonds. This distinction can save time when an animation seems not to affect the objects you selected.
Build the reveal on the timeline
With the desired nodes selected, double-click Appear in the Animation panel of the Animator. The effect is made up of four keyframes, which define the stages of the reveal:
- Keyframes 1–2: the selected nodes are fully transparent.
- Keyframes 2–3: the nodes progressively appear as their transparency decreases.
- Keyframes 3–4: the nodes are fully opaque, with no transparency.
This sequence gives you a practical way to think about timing. The first interval establishes that the nodes are not yet visible. The middle interval is the actual reveal. The final interval holds the nodes in their fully visible state. Move the keyframes as needed to change when these stages happen and how much timeline space the transition occupies.
For a clear presentation, decide what the audience should notice before adjusting the timing. If one model is the focus, reveal it after the scene’s other elements are already understandable. If several selected nodes should appear together, apply the effect to those nodes as a group. These are presentation choices rather than extra animation settings, but thinking them through can make the result easier to read.
Shape the feel of the transition
The change between frames does not have to feel uniform. You can modify the easing curve to change how the animation parameters are interpolated between frames. In other words, the curve affects the progression of the transition, while moving the keyframes changes its timing on the animation timeline. Try adjusting one at a time so you can judge whether the reveal feels too sudden, too slow, or appropriately paced for the scene.
Appear is also distinct from Show. For nodes without a transparency attribute, Appear behaves similarly to Show; those nodes do not receive the same transparency-based fade. Keep this limitation in mind when mixing different kinds of nodes in one presentation.
One interface note: older instructional material may refer to an Animation menu. In the current workflow described in the documentation, animations are accessed through the Animation panel in the Animator, and presentation actions are available through the Animator’s controls.
For details and related animation options, see the Appear animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.