A molecular scene can contain exactly the right structures and still be difficult to follow. When everything is visible at once, viewers may not know where to look—or which part of the model is being introduced. A gradual reveal can make a presentation easier to read by bringing selected structures into view over time.
In SAMSON, the Appear animation progressively changes the transparency of selected nodes. It is useful when you want to introduce a model, visual object, mesh, or label without showing it immediately at full opacity. Think of it as a way to manage the audience’s attention, not just as a decorative effect.
Start with the right nodes
Before adding the animation, select the nodes you want to reveal. This detail matters for molecular structures: individual atoms and bonds do not have their own opacity attribute. Their structural models do. To change the transparency of atoms and bonds with Appear, apply the animation to the relevant structural model, rather than to individual atoms or bonds.
Appear can be applied to nodes that have a transparency attribute, including structural models, visual models, meshes, and labels. For nodes without that attribute, the animation behaves similarly to Show. So if the result is an immediate show/hide-style change rather than a transparency transition, check which node type you selected.
Build a reveal with four keyframes
To add the effect, choose the nodes, then double-click Appear in the Animation panel of the Animator. The animation uses four keyframes to define the sequence:
- Keyframes 1–2: the selected nodes are fully transparent.
- Keyframes 2–3: they progressively appear as their transparency decreases.
- Keyframes 3–4: they remain fully opaque, with no transparency.
You can move the keyframes to adjust where these stages fall in your animation. That gives you a practical way to control the pacing: leave a structure unseen for longer, make its reveal occupy more of the sequence, or bring it to full opacity sooner. The keyframes can be moved whenever you need to refine the timing.
A simple planning method
For a clearer presentation, decide what the viewer should notice first. Apply Appear to that node or structural model, then consider what should remain visible while the next element is introduced. If you are revealing several parts of a scene, treating each reveal as a separate communication decision can help prevent the animation from becoming visually busy.
Also consider how the transition should feel. The animation’s easing curve changes how parameters are interpolated between frames. Adjusting it can help shape the character of the transition, while the keyframe positions determine where its stages occur.
The documentation includes an example of the Appear and Disappear animations:
A useful final check is to confirm that the selected nodes are the ones whose transparency you intend to change—especially when working with atoms and bonds—and then review the reveal’s timing in the Animator. For details, see the Appear animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.