In molecular modeling, clarity is essential. Whether you’re preparing a presentation, building an educational video, or comparing structural conformations, the ability to highlight changes in your models can make a major difference. A frequently encountered challenge among modelers and educators is how to visually emphasize the appearance or disappearance of specific molecular elements over time, without affecting their transparency or altering the model’s visual consistency.
If you’ve ever needed to cleanly show molecules or atoms appearing and disappearing in synchrony with an explanatory narrative or data change, the Flash animation effect in SAMSON provides a helpful solution.
What Is the Flash Animation?
Unlike animations that adjust transparency, the Flash animation manipulates the visibility of chosen nodes (atoms, molecules, groups, etc.). This allows nodes to stay invisible during parts of the animation and become instantly visible at specific moments, before disappearing again. This is perfect for emphasizing key transitions in a molecular process without clutter.
Why Use It?
Let’s say you are modeling an allosteric mechanism, and want students or collaborators to notice when a regulatory molecule binds and disappears. Or perhaps you’re comparing two states of a protein and simply want parts of the earlier state to cleanly flash out while the new ones flash in. The Flash animation enables a timed, clean toggle of molecular components that is both intuitive and visually effective.
How It Works
To use the Flash animation in SAMSON:
- Select the nodes you want to flash (appear and disappear).
- Double-click on the Flash effect in the Animation panel.
- SAMSON will generate four keyframes. Here’s what happens:
- Keyframes 1-2: Nodes stay hidden.
- At keyframe 2: Nodes appear suddenly.
- Keyframes 2-3: Nodes stay visible.
- At keyframe 3: Nodes disappear.
- Keyframes 3-4: Nodes stay hidden again.
The keyframes can be dragged along the timeline to adapt the timing of the appearance/disappearance effect, giving you control over exactly when things should flash in or out.
Bonus: Smooth Transitions With Easing Curves
Even if the visibility toggles are sudden, the Easing curve can be adjusted to control how SAMSON interpolates the parameters over time. While this might not directly affect node visibility in Flash, combining easing curves with other effects can help integrate Flash into more complex animations more seamlessly.
Visual Example
Here’s what the Flash animation looks like in action:
When to Use Flash vs Other Effects
Consider Flash as a good option when:
- You need abrupt appearance/disappearance for clarity.
- You want to sync structural display with narration or a visual story.
- You’re showing transient molecular interactions.
For slower, more gradual transitions, effects like Appear or Pulse might be more appropriate. But for moments when you need things to show up and vanish like a spotlight cue, Flash is reliable and precise.
To learn more about using the Flash animation in SAMSON, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/flash/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.