When creating molecular presentations or simulations, one of the biggest challenges scientists face is guiding the viewer’s attention to specific events. Sometimes, molecules are added or removed, or key regions switch configurations. These changes are important but can easily get lost in a complex molecular system. This is where SAMSON’s Flash animation can become a simple yet effective solution.
The Flash animation is designed to make selected nodes (such as molecules, atoms, or molecular fragments) appear and disappear in a timed sequence. Unlike animations that slowly fade in or out using transparency, Flash manipulates the visibility of objects directly—making them suddenly pop in and out of view. This can make critical changes in your molecular system more noticeable without overloading the visual field.
Why Use Flash?
Imagine you’re explaining the binding of a ligand to a protein. The moment the ligand appears should be striking—your audience shouldn’t have to search for it. Or perhaps you want to demonstrate the disappearance of a water shell during a conformational change. Instead of gradually blending it away, you’d rather have it vanish clearly when the conformational shift occurs. Flash animation achieves exactly that, with simple controls and minimal setup.
How It Works
The Flash animation comes with four keyframes:
- Keyframes 1 → 2: nodes remain hidden
- Keyframe 2: nodes become visible
- Keyframes 2 → 3: nodes remain visible
- Keyframe 3: nodes become hidden again
- Keyframes 3 → 4: nodes remain hidden
You can move these keyframes to control the timing of the appearance/disappearance. This makes it straightforward to coordinate the Flash animation with other elements in your timeline—for example, combining visibility changes with camera movements or diagram overlays.
Customizing the Timing
To fine-tune how quickly changes happen, you can modify the easing curve of the Flash animation. This lets you create smoother or more dramatic transitions, depending on your presentation style. You’ll find adjustment options in the Inspector panel once the Flash animation is selected.
How to Add the Flash Animation in SAMSON
- Select the nodes you want to make appear/disappear.
- Go to the Animation panel within the Animator.
- Double-click on the Flash effect.
- Adjust the keyframes in the timeline to determine when the visibility changes happen.
- Fine-tune the easing settings if desired.
This quick setup can make your presentations clearer and your explanations more compelling. Viewers won’t miss what’s important on-screen—especially helpful in teaching, paper supplements, or collaborating with colleagues from other disciplines who may not be familiar with your system.
To learn more, visit the original SAMSON Flash animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.