A molecular scene can contain more information than a viewer can take in at once. When several structures or selected regions are visible together, it may be difficult to focus attention on the part being discussed. A timed reveal can help: show a chosen set of nodes for a defined part of an animation, then hide them again.
In SAMSON, the Flash animation changes node visibility. It does not change transparency. That distinction matters: Flash is suited to a clear switch between hidden and visible states, not a gradual fade. If you want a scene element to appear as a step in a narrated explanation or presentation, this can keep the visual change easy to read.
Plan the moment, not just the effect
Before adding the animation, decide which nodes should flash and what the audience should notice while they are visible. For example, you might use a selected part of a molecular scene as a temporary point of focus, then return to the surrounding view. Keeping the animated selection purposeful helps avoid replacing one crowded scene with a different kind of visual distraction.
To set it up, first choose the nodes you want to show and hide. Then double-click Flash in the Animation panel of the Animator. The effect has four keyframes:
- Between keyframes 1 and 2, the chosen nodes stay hidden.
- At keyframe 2, they become visible and remain visible between keyframes 2 and 3.
- At keyframe 3, they become hidden and remain hidden between keyframes 3 and 4.
This sequence gives you more control than a single on/off event: the keyframes define a hidden interval, a visible interval, and another hidden interval. Consider where the visible interval falls in relation to the surrounding animation. If it begins too early, the reveal may compete with the previous moment; if it ends too soon, viewers may not have time to inspect the selected nodes.
Adjust timing after you add it
You can move the animation’s keyframes as needed. This makes it possible to adjust when the selected nodes appear and disappear without treating the initial placement as final. A practical review is to play the animation and check three things: whether the hidden opening gives enough context, whether the visible interval lasts long enough to understand the highlighted content, and whether the final hiding happens at a useful point.
The Inspector also lets you change the easing curve, which changes how parameters are interpolated between frames. Because Flash uses visibility rather than transparency, do not expect the nodes to fade gradually in or out. Think of the effect as a timed visibility change, and use the keyframes to place that change in the sequence.
When choosing an animation, start from the communication goal. If the goal is to briefly expose selected nodes and then remove them from view, Flash offers a compact, editable sequence. If you need a different kind of appearance or disappearance, SAMSON’s animation documentation also lists related effects such as Appear, Disappear, Show, Hide, and Pulse.
For the exact setup steps and animation properties, see the Flash animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.