When presenting molecular mechanisms, one challenge researchers often face is how to draw attention to key events or components without overwhelming the viewer with too much visual information. Whether it’s emphasizing a cofactor binding, a sudden conformational change, or the moment a ligand appears, timing and visibility are crucial to make the science clear.
In molecular modeling and visualization, static images can miss the dynamics. But what if you could briefly flash important parts into view—just at the right time—to let the viewer focus exactly where you need them to?
Introducing the Flash Animation in SAMSON
The Flash animation effect in SAMSON is designed exactly for that. This simple animation toggles a selection of nodes—such as atoms, molecules, or anything else—so that they appear at a specific keyframe and disappear shortly after. It’s handled through visibility (not transparency), making it a clean visual cue without distractions.
Here’s how it works: once applied through the Animation panel, the Flash animation controls the visibility of selected nodes over four keyframes:
- Keyframes 1 → 2: the nodes are hidden.
- At keyframe 2: the nodes become visible.
- Keyframes 2 → 3: the nodes stay visible.
- At keyframe 3: the nodes become hidden again.
- Keyframes 3 → 4: the nodes remain hidden.
You can move these keyframes around to control exactly when the event happens in your animation. And if you want to fine-tune how the visibility changes between keyframes, SAMSON also lets you adjust the easing curve of the animation.
Why Use Flash?
Imagine you’re showing the transport of a molecule through a membrane channel. Rather than showing it continuously, flashing the molecule at the moment it enters and then again when it exits can simplify the story and avoid visual overload elsewhere.
Or consider a large protein-ligand complex: flash the ligand into visibility the moment the binding pocket opens. It can serve as a concise cue for something important happening—without having to interrupt your presentation.
This approach is especially useful when you want to convey presence or absence in a binary way. Since Flash is based on visibility instead of transparency, there’s no ambiguity about whether something is present or just faint.
How to Add It
To add a Flash animation, simply:
- Select the nodes you want to animate.
- Double-click on Flash in the Animation panel in SAMSON’s Animator.
- Adjust the keyframes to the timing you need.
Optional Customization
To further customize the animation timing and feel, you can explore the Easing curve settings in the Inspector panel. This allows interpolation tweaks between keyframes—useful for syncing with other animation effects.
In presentations or educational settings, the Flash animation is one of the more subtle but powerful tools to direct viewer attention momentarily—something video editors refer to as building “focus”.
Learn more and see detailed steps in the official documentation: Flash Animation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.