When creating molecular animations for research presentations, teaching materials, or publications, one recurring challenge is directing the viewer’s attention at the right moment. In complex molecular systems, it can be unclear which atoms or structures are meant to take center stage. This is especially true when comparing different molecular conformations, or showing steps in a reaction mechanism.
The Flash animation option in SAMSON, the integrative molecular design platform, offers a simple but effective solution to that problem. It allows users to make certain parts of their molecular system suddenly appear, stay visible for a short time, and then disappear—helping to draw attention exactly when and where it’s needed without cluttering the scene.
What Does the Flash Animation Do?
The Flash animation isn’t just about blinking structures in and out of existence. It manipulates the visibility of specific nodes—atoms, molecules, surfaces, or more—without changing their transparency. This means that the nodes are either fully shown or completely hidden, making the transitions sharp and easy to follow.
This clarity makes the Flash animation particularly useful in scenarios such as:
- Revealing binding pockets momentarily during a ligand docking animation
- Showing intermediates in a reaction mechanism for a short duration
- Highlighting supporting structures or domains without overwhelming the main focus
How It Works
The Flash animation consists of 4 keyframes:
- Keyframes 1 to 2: The selected nodes remain hidden
- At Keyframe 2: The nodes become visible
- Keyframes 2 to 3: The nodes stay visible
- At Keyframe 3: The nodes are hidden again
- Keyframes 3 to 4: Nodes remain hidden
This simplicity makes it easy to “punctuate” your animation timeline with meaningful visual cues. You just choose the nodes you want to animate, double-click the Flash effect in the Animation panel, and then arrange the keyframes according to your narrative needs.
Keyframes are completely editable, and users can fine-tune timing by dragging them along the timeline. This allows for precise control of when things appear and disappear—ideal for synchronizing with narration in a video or timing in an interactive lesson.
Refining the Behavior
Want smoother or snappier transitions? You can adjust the Easing curve that defines how properties interpolate between keyframes. While the Flash animation itself contains mostly on/off transitions in visibility, easing control lets you better sync the animation’s overall flow with other effects or animations in the same scene.
When to Use Flash (and When Not To)
Flash works best to punctuate key moments. If your goal is to gradually reveal a structure (such as fading in a protein surface), another animation like Appear might be more appropriate. But if you need a clean visual cue—”here’s something to notice”—Flash is ideal.
To learn more and explore examples, visit the original documentation page: 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.