When preparing molecular animations for presentations, publications, or teaching, one common challenge is how to clearly emphasize the appearance and disappearance of specific molecular components without overwhelming the viewer. Often, researchers find it difficult to control exactly when and how key elements of their models become visible or invisible — especially across multiple scenes or stages of a simulation.
The Flash animation in SAMSON offers a simple yet highly effective solution to this problem. If you’re working with molecular models and want to selectively highlight atoms, molecules, or assemblies in a clean and repeatable way, this feature can help you do just that — all while keeping your animations intuitive and focused.
What is the Flash Animation?
The Flash animation makes selected nodes (such as atoms or groups) appear at a chosen keyframe and disappear at another. Importantly, this is done by toggling visibility — not transparency — which helps avoid the visual clutter often introduced by semi-transparent structures in complex molecular scenes.
When to Use It
Here are some practical scenarios:
- Emphasize the binding of a ligand by making the ligand flash into the scene exactly when binding begins.
- Demonstrate conformational changes by introducing structural elements at specific stages.
- Guide attention during educational videos by using a flash effect to highlight active sites or mutations.
How It Works
To use the Flash animation in SAMSON:
- Select the nodes you want to flash (appear and disappear).
- Open the Animation panel within the Animator.
- Double-click on the Flash effect to add it to your animation timeline.
- The animation applies over 4 keyframes:
- Keyframes 1–2: Nodes are hidden.
- Keyframe 2: Nodes become visible.
- Keyframes 2–3: Nodes stay visible.
- Keyframe 3: Nodes become hidden again.
- Keyframes 3–4: Nodes remain hidden.
- You can then move these keyframes as needed to align with your storyline.
You can further refine the visibility transitions using the Easing curve, available in the Inspector. This changes how the animation looks between keyframes — making the effect smoother or more discrete, depending on your preferences.
This is especially useful when you want the appearance or disappearance of nodes to follow a more natural tempo — for example, mimicking a signaling event or an induced fit mechanism.
Why It Matters
Animations should support your message — not obscure it. Using Flash lets you tell a clearer story by highlighting what’s important only when it’s important. Compared to simply fading things in or out with transparency, toggling visibility avoids visual confusion and helps maintain focus.
To learn more and explore related animation effects such as Appear, Disappear, Pulse, and Show, 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 download and start using SAMSON at https://www.samson-connect.net.