Creating engaging molecular animations is often essential when preparing scientific presentations, tutorials, or visualizations for molecular modeling projects. One recurring challenge is how to briefly yet clearly showcase the appearance and disappearance of molecular components—without overwhelming the viewer with effects like fades or morphs. In these cases, clarity wins over complexity.
This is where the Flash animation effect in SAMSON comes in. The Flash animation allows molecular modelers to emphasize key molecular structures by making them appear at a selected keyframe and then vanish at another, without transitions based on transparency. This keeps things clean: you either see it, or you don’t.
Why does this matter?
In communicative science visuals, timing and simplicity are powerful. Suppose you’re showcasing part of a protein’s active site or visualizing a ligand binding interaction. You may want a sidechain or a cofactor to stay hidden at first, appear briefly when relevant, and then disappear again—fast and without visual clutter. The Flash effect is ideal here.
How it works
To apply the Flash animation in SAMSON:
- Select the set of nodes (atoms, residues, molecules, etc.) that you want to show temporarily.
- Open the Animator’s Animation panel and double-click on the Flash animation effect.
By default, this will create four keyframes:
- Frames 1–2: nodes stay hidden.
- At frame 2: nodes appear and stay visible between frames 2–3.
- At frame 3: nodes disappear again and remain off between frames 3–4.
Here’s a visual example of how it looks in action:
Controlling timing with Easing Curves
Another nice touch is that you can fine-tune how the transition timing behaves between the keyframes using an easing curve. While this may seem subtle, adjusting the curve allows for a better sense of pacing. For example, having elements appear quickly but disappear slowly—or vice versa—can help direct viewer attention more effectively.
Use case suggestions
- Highlighting critical binding interactions: briefly show a ligand during its binding frame.
- Guiding the viewer’s attention during a walkthrough: Flash only the region of interest at the right moment in your animation.
- Visual contrasts in dynamic processes: make catalytic residues momentarily visible during a simulated reaction pathway.
While the effect is simple, its utility is high—especially when you need to drive attention clearly from one molecular feature to another, without relying on more complex animated transitions.
To learn more and explore additional options, read the full documentation 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 here.