Communicating complex molecular mechanisms often requires more than static images. Whether you’re creating molecular tutorials, preparing research presentations, or simply trying to make your findings clearer to non-specialists, animation can make a real difference. But not all animations are about smooth motion or fancy effects. Sometimes, what you really need is precise visibility control: showing key parts of a molecule at the right moment without unnecessary distraction. This is where the Flash animation in SAMSON can help.
Why Visibility-Based Animation Matters
Transparent atoms aren’t always the best solution when you need clarity. The Flash animation allows you to cleanly make selected molecular nodes appear and disappear without altering their transparency, making it perfect for emphasizing or de-emphasizing molecular elements throughout your animation.
If your molecular scene has a crowded landscape—enzymes, ligands, water molecules, ions—you might want to highlight just one region or track a specific interaction. Flash makes that straightforward, enabling focus by toggling visibility at key moments.
How the Flash Animation Works
To use Flash, first select the nodes—atoms, groups, surfaces, etc.—that will be controlled. Then, double-click the Flash animation effect in the Animation panel under the Animator.
Flash is built around four keyframes:
- Between keyframes 1 and 2: nodes are hidden
- At keyframe 2: nodes appear and remain visible between keyframes 2 and 3
- At keyframe 3: nodes disappear, staying hidden through keyframe 4
This simple structure gives you fine control over when things become visible or invisible in your timeline. You can move these keyframes to adjust timing precisely—for example, to line up with verbal explanations in a narrated video or to match transitions in a slideshow.
Fine-Tuning the Animation with Easing Curves
You can adjust how smoothly the visibility toggles happen by modifying the easing curve. This won’t affect transparency or movement—since Flash deals only with visibility—but it can affect how the timing feels: immediate vs. accelerated or decelerated visibility.
When to Use Flash
Consider these scenarios where Flash can be especially helpful:
- To introduce a ligand into a binding pocket only at the right moment in a molecular animation
- To momentarily hide side chains or water molecules while explaining structural motifs
- To switch between alternative conformations or different parts of a reaction pathway
Flash is a to-the-point, visibility-based tool for communicators and researchers who want clean, distraction-free molecular animations.
Learn more in the official documentation: Flash Animation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.