A molecular scene can contain more detail than an audience needs to see all at once. Showing every component from the start may make it harder to follow a structural explanation, while manually hiding and showing nodes at different moments can be tedious. The Flash animation offers a simple way to stage visibility: selected nodes are hidden, shown for a portion of the animation, then hidden again.
This is useful when you want to direct attention to a particular part of a molecular model without changing the model itself. For example, you might show a selected group briefly while presenting a step in your explanation, then remove it from view so the next part of the scene is easier to read. These are visibility changes, not transparency changes: the nodes appear or disappear rather than becoming gradually see-through.
Build a focused reveal
Start by selecting the nodes you want the animation to affect. Then, in the Animator, double-click Flash in the Animation panel. The effect uses four keyframes to define a simple sequence:
- Keyframes 1–2: the selected nodes stay hidden.
- At keyframe 2: the nodes become visible, and they stay visible between keyframes 2 and 3.
- At keyframe 3: the nodes become hidden, and they stay hidden between keyframes 3 and 4.
In practical terms, the middle interval is the moment when the selected part of the scene is available to the viewer. Before and after it, that part is out of sight. This makes Flash a good fit for a brief, deliberate reveal rather than a gradual fade.
Use keyframe placement to shape the timing
The default sequence is only a starting point. You can move the animation’s keyframes to suit the pace of your presentation. If the visible interval needs to last longer, adjust the spacing around the portion between keyframes 2 and 3. If the reveal should happen earlier or later, move the relevant keyframes along the animation. The keyframes can always be moved, so you can refine the timing after previewing the scene.
A useful way to plan the effect is to decide three things before adjusting it: what should remain hidden at first, what should be revealed, and when that revealed content should leave the scene. Keeping the selection limited to the nodes needed for that moment helps the visibility change stay purposeful. If unrelated nodes are included in the selection, they will also be affected by the animation.
Visibility is not transparency
Flash controls whether nodes are visible. It does not make them transparent. That distinction matters when a molecular presentation depends on the appearance of the selected nodes themselves: Flash removes them from view during its hidden intervals rather than leaving them faintly visible. If your goal is a staged on/off reveal, this behavior is direct and predictable. If your goal is a transparency effect, Flash is not described as providing that effect.
Fine-tune the animation
The Inspector provides access to the animation options, and you can change how parameters are interpolated between frames by modifying the Easing curve. Consider reviewing the result after changing keyframe positions or the easing curve, so the sequence fits the rhythm and clarity of your explanation. The key idea is to use the visible interval intentionally: long enough for the audience to notice the selected structure, then hidden when it is no longer needed.
For the complete instructions, see the Flash animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.