Creating molecular animations often involves showing or hiding specific atoms, residues, or molecular structures across time. But if you’re changing visibility in a manual, step-by-step process, it can quickly become tedious—especially if you’re trying to time these changes precisely in a presentation or video.
The Flash animation in SAMSON is designed to solve this: it automates the appearing and disappearing of selected nodes at specific keyframes, making it easier to focus attention on a region of interest with minimal setup. Rather than manipulating transparency or visibility manually, Flash handles it for you across four keyframes.
Why modelers use Flash
This feature is especially useful when you want to momentarily highlight a specific molecule, atom, or group during an animation—perhaps to demonstrate its mechanism of action or its role in a biological pathway. Rather than keeping that object visible throughout the animation, which may clutter the scene, Flash makes the object visible only when needed.
Here’s how it works:
- Keyframes 1–2: The selected nodes remain hidden.
- Keyframe 2: The nodes become visible.
- Keyframes 2–3: The nodes stay visible.
- Keyframe 3: The nodes become hidden again.
- Keyframes 3–4: The nodes stay hidden.
Getting started with Flash
To set up this animation, follow these steps:
- Select the node(s) you want to animate. These can be atoms, groups, molecules, etc.
- Open the Animation Panel inside the Animator.
- Double-click on the Flash animation effect.
- You’ll now see the four keyframes described above automatically created.
- Adjust the timing by simply moving these keyframes in the Animator timeline.
Adjusting the animation curve
If you wish to control how sudden or smooth these transitions are, you can modify the Easing curve within the property settings of the animation. This allows further control over how the visibility change behaves, although for Flash, the change in visibility is instantaneous and does not transition gradually like opacity might.
Flash is a useful tool when you want to emphasize a specific part of a molecular system without cluttering your entire animation. Whether you’re building a scientific presentation, a teaching video, or just trying to better understand a molecule’s function visually, using Flash can help direct attention exactly where it’s needed, exactly when it’s needed—with very little effort.
You can learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.