When a molecular model contains several components, viewers may struggle to see which group matters at a particular moment. Hiding and showing nodes at carefully chosen points in an animation can make a presentation easier to follow—without changing the structure itself. In SAMSON, the Flash animation provides one way to do this.
Flash changes the visibility of selected nodes. It does not animate their transparency, so the nodes switch between hidden and visible rather than gradually fading. That distinction matters: use Flash when you want a clear on/off reveal, not a soft transition.
Plan the reveal before you animate
Start by deciding what the audience should see first, what should appear next, and what should no longer be visible afterward. For example, you might keep one selected group out of view while introducing the rest of a scene, show that group for a specific part of the presentation, and then hide it again. This is a visual storytelling choice—not a representation of a molecular event or a change in the model’s physical state.
Once you have a simple sequence in mind, select the nodes you want Flash to control. Then double-click Flash in the Animation panel of the Animator. The animation uses four keyframes, with the selected nodes hidden between keyframes 1 and 2, visible from keyframe 2 through the interval to keyframe 3, and hidden again from keyframe 3 through keyframe 4.
This four-keyframe structure gives you a useful mental model: hidden → visible → hidden. The keyframes mark when those states change; moving them lets you adjust when the reveal begins and how long the visible interval lasts. If the reveal feels too brief for someone to inspect, move the relevant keyframes to give it more time. If it interrupts the flow, adjust their positions to better fit the surrounding animation.
Keep the visual message clear
A few practical checks can help prevent confusion:
- Choose the smallest useful selection. Flash affects the nodes you select, so check the selection before adding the animation. A broad selection may hide more of the scene than intended.
- Make the visible interval purposeful. Give viewers enough time to recognize the revealed group, especially if the scene is dense or the animation is being used to explain a sequence.
- Preview the transitions in context. A visibility change can feel abrupt by design. Watch it alongside the surrounding animation to make sure the cut supports the explanation rather than distracting from it.
- Use a different approach if you need a fade. Because Flash operates through visibility rather than transparency, it is not the tool for gradually fading nodes in or out.
You can move the animation’s keyframes as needed. The Inspector also lets you change how parameters are interpolated between frames by modifying the easing curve. Since Flash is based on visibility changes, check the result in the animation rather than assuming an easing adjustment will turn the switch into a transparency fade.
Flash is most useful when your presentation needs a deliberate, timed appearance and disappearance of selected nodes. A clear selection and well-placed keyframes can help direct attention while keeping the underlying molecular scene intact. For the full instructions, see the Flash animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.