Molecular animations play a key role in understanding and presenting structural changes, interactions, or sequences occurring within complex molecular systems. But not every animation should be overly complex. Sometimes, you simply need to draw attention to specific parts of the model—at the right time, and just for a moment. This is where the Flash animation in SAMSON can be especially helpful.
If you’re trying to highlight a ligand binding event, a reaction center, or an important structural motif appearing momentarily in a simulation, the Flash animation lets you do so clearly without cluttering your visual timeline or resorting to transparency tricks. It’s designed to make nodes (molecular components) appear and disappear based purely on their visibility, not their transparency settings. This ensures that your viewers are not distracted by see-through elements or fading objects—they simply see the important parts, when it matters.
How Flash Works in SAMSON
The Flash animation includes four keyframes that define when the selected nodes are visible or hidden:
- Keyframes 1 → 2: Nodes stay hidden
- Keyframe 2: Nodes become visible
- Keyframes 2 → 3: Nodes remain visible
- Keyframe 3: Nodes become hidden again
- Keyframes 3 → 4: Nodes remain hidden
This simple timing structure allows you to effectively insert a brief highlight—almost like blinking a spotlight on a part of your molecular system—without requiring complicated transitional effects. For example, to direct your audience’s attention to a crucial binding site just before a major conformational change, you could add a Flash effect right before a morphing sequence.
How to Add the Flash Effect
Start by selecting the nodes you want to emphasize. These might be residues, functional groups, ligands, cofactors—anything with structural or functional relevance at that moment in your animation. Then:
- Double-click on the Flash effect in the Animation panel.
- Adjust the keyframes as needed to control the timing of the visibility.
- Fine-tune the appearance of the animation using the easing curve via the Inspector if you need smoother transitions.
Although Flash doesn’t rely on transparency, it draws its strength from clarity and timing. In group presentations, scientific talks, or tutorials, this minimal approach can make your message more comprehensible, especially when combined with other animations like morphing or rotation.
Why Use Flash Over Other Visibility Tools?
You might wonder how Flash compares to other visibility-related animations in SAMSON, such as Appear or Disappear. Unlike these other effects, Flash is designed specifically for temporary emphasis. For example, if you’re presenting a “before and after” transformation and want one component to briefly appear in the timeline just to introduce it—the Flash animation is purpose-built for that use-case. It allows for minimal intrusion in the visual sequence while still making the moment count.
In summary, Flash is ideal for:
- Highlighting brief molecular events
- Drawing temporary attention to structural components
- Enhancing the clarity of complex demonstrations
- Controlling node visibility without impacting scene transparency
It’s a small tool that can vastly improve how audiences understand your animations, especially when paired with clear narrative timing.
To learn more, visit the original documentation page for the Flash animation here: https://documentation.samson-connect.net/users/latest/animations/flash/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.