When crafting molecular animations, a common challenge faced by modelers is how to emphasize key events—such as the binding of a ligand or the disappearance of a residue—without overwhelming the viewer with continuous motion. Sometimes, less is more.
The Flash animation effect in SAMSON provides a solution: it lets you make one or more molecular components appear and then disappear precisely, drawing attention to specific structural changes. This avoids fades or long transitions and instead gives complete visual focus—like a spotlight—for a brief moment in your animation timeline.
What is the Flash animation?
The Flash animation offers a way to make selected molecular nodes visible for a short period within a timeline, without relying on transparency. It’s like visually switching something on and off, at specific moments, to tell a compact, clear story. This is especially helpful for visualizing:
- A mutation site appearing at a specific moment
- A cofactor suddenly binding to its protein
- A structural change only noticeable briefly
Step-by-step: How to add it
Here’s how to use the Flash animation in SAMSON:
- Select the nodes (e.g., molecules, residues, atoms) you want to make appear and disappear.
- In the Animation panel of the Animator, double-click on the Flash effect.
This inserts an animation with four keyframes:
- Keyframes 1 to 2: nodes remain invisible
- At Keyframe 2: nodes become visible
- Keyframes 2 to 3: nodes stay visible
- At Keyframe 3: nodes become hidden again
- Keyframes 3 to 4: nodes stay hidden
You can drag these keyframes along the timeline to choose exactly when the flashing occurs.
Use Case Example
Let’s say you want to show a ligand binding event that is hidden at first, then briefly appears, and then disappears again. This could help draw the viewer’s attention to the ligand without distracting from other parts of the animation. Add a Flash animation on the ligand itself, align the keyframes with your main animation timeline, and your highlight will stand out naturally.
Tweaking the Feel with Easing Curves
Visual timing can make a big difference. In the Inspector, you can modify the Easing curve to decide how the change between frames is interpolated. Although the Flash animation deals with visibility (a binary attribute), easing options can still control how transitions between rest and motion unfold for other attributes you animate simultaneously.
Why use Flash instead of Show/Hide?
The difference is timing control. Where Show and Hide simply toggle visibility, Flash lets you weave visibility control into your timeline using precise keyframes. It creates a clean and discrete pattern, perfect for short-lived visual emphasis.
If you’re preparing a molecular presentation, paper supplement, or teaching material, Flash can help control pacing and direct attention intuitively.
To learn more, visit the official 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 for free at https://www.samson-connect.net.