When showcasing molecular systems—whether for teaching, publications, or collaboration—communicating clearly is essential. One often-overlooked challenge is ensuring your audience knows where to look. Complex molecules or large assemblies can be visually overwhelming, especially when everything appears at once.
This is where the Flash animation effect in SAMSON can help. This feature provides a simple but useful way to temporarily highlight parts of your molecular model by making them appear and disappear at defined times. What’s unique about Flash is that it manipulates visibility directly—not transparency—so there’s no confusion with semi-transparent objects remaining in view.
Why Use Flash?
Whether you’re creating an educational animation to explain protein domains or preparing a simulation walkthrough to highlight a ligand binding event, drawing temporary focus to a subset of atoms or molecules is a helpful visual strategy. Flash allows you to:
- Guide the viewer’s attention to specific molecular features.
- Control visual flow across a timeline without clutter.
- Create blinking effects or synchronized appearances with other animations.
How It Works
The Flash effect works with nodes, which are SAMSON’s way of organizing molecular objects. Here’s how the animation behaves across its four keyframes:
- 🔹 Between keyframes 1 and 2: nodes remain invisible.
- 🔹 At keyframe 2: nodes become visible.
- 🔹 Between keyframes 2 and 3: nodes stay visible.
- 🔹 At keyframe 3: nodes become hidden again.
- 🔹 Between keyframes 3 and 4: nodes remain hidden.
This makes it a great tool for a quick visual pulse or spotlight within a longer animation sequence.
Getting Started
1. Select the atoms, residues, molecules or other nodes you want to feature.
2. Open the Animation panel in the Animator workspace.
3. Double-click the Flash effect.
4. Adjust the resulting four keyframes to place the flash timing wherever you need it in your animation.
Need the flashing to happen earlier or later? No problem. You can move any of the keyframes along the timeline. This flexibility allows you to sync the visibility pulse with other actions.
Extra Control with Easing Curves
If you plan to chain Flash with other animations or want smooth timing transitions, you can modify how parameters change between frames using Easing curves. This lets you soften or sharpen transitions at high precision.
When to Avoid It
Because Flash isn’t using transparency, the region your nodes occupy will disappear completely when hidden. If you’re trying to achieve a fading effect instead of a sudden appearance/disappearance, consider alternatives like the Pulse or Appear effects. Each animation option in SAMSON offers different visual outcomes for different narrative purposes.
To learn more, visit the full documentation page for Flash here: https://documentation.samson-connect.net/users/latest/animations/flash/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.