When preparing molecular animations for presentations or educational content, one common challenge is directing the viewer’s attention at the right moment. Whether you’re showing a ligand docking, a conformational shift, or any event that happens within a complex molecular system, the key is clarity: what happens, where, and when?
That’s where the Flash animation in SAMSON can help. This simple yet effective tool allows you to make specific elements of your molecular scene quickly appear and disappear, drawing the viewer’s eye right when needed — like highlighting a synapse of activity in the middle of a larger molecular assembly.
What Does the Flash Animation Do?
The Flash effect is different from using transparency or motion. It controls the visibility of selected nodes (which could be molecules, molecular groups, labels, or any object in your scene) between specific keyframes.
This is especially useful when you need to:
- Draw attention to an active site just before a reaction.
- Illustrate transient interactions, such as hydrogen bonds during a simulation.
- Show a ligand appearing right when docking is completed.
- Minimize visual clutter by temporarily hiding parts of the system.
How It Works
The animation assigns 4 keyframes with specific visibility instructions:
- From keyframe 1 to 2: nodes stay hidden.
- At keyframe 2: nodes become visible.
- Between keyframe 2 and 3: nodes stay visible.
- At keyframe 3: nodes become hidden again.
- Between keyframe 3 and 4: nodes remain hidden.
This visibility-only approach does not rely on transparency interpolation and works well in conjunction with other animation effects (e.g., movement, rotation).
How to Add This to Your Animation
1. Start by selecting the nodes you want to control (atoms, molecules, labels, etc.).
2. In the Animation panel of the Animator, double-click on the Flash effect.
3. SAMSON automatically creates the 4 keyframes mentioned above. You can adjust their position on the timeline to synchronize with other events in your scene.
4. You can also edit the easing curve of the animation (e.g., linear or smooth in/out visibility changes), although for Flash it’s usually not necessary since visibility changes are typically abrupt.
Why Use It?
The Flash animation is useful anytime you want to inject a visual cue — it acts like a momentary spotlight turned on and off. And because it operates on visibility alone, it avoids performance issues linked to rendering transparency or extra geometry.
If you’re preparing visuals for a lecture, publication, or video report, Flash gives you an efficient way to present complex molecular behavior in a clear and sequential way. Need the receptor to vanish so the ligand path is obvious? Want a product molecule to appear right after a simulated reaction step? Flash handles that with just a few clicks.
It helps you fine-tune your viewer’s attention span to what matters, exactly when it matters.
To learn more, visit the official Flash animation documentation: https://documentation.samson-connect.net/users/latest/animations/flash/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform at https://www.samson-connect.net.