If you’ve ever spent time crafting molecular animations to convey a complex process — say, ligand binding or conformational change — you might have noticed that visual clarity is just as important as scientific accuracy. Too many objects on the screen can distract from the key message. One common need among molecular modelers is to cleanly show and hide relevant molecular entities at precise moments in an animation. That’s where the Flash animation effect in SAMSON comes in.
The Flash animation allows you to control the visibility of selected molecular nodes between specific keyframes in your animation timeline — without changing their transparency or position. This is particularly helpful when you want to direct a viewer’s attention over time in a tutorial, a scientific presentation, or even a publication video abstract.
What is the Flash Animation?
The Flash animation in SAMSON makes selected nodes visible at a specific point in time and invisible again later. This differs from animations like Fade, which use transparency; Flash uses raw visibility toggling — things either appear or they don’t.
Here is the overall animation behavior across four keyframes:
- Keyframes 1 → 2: Nodes stay hidden
- At Keyframe 2: Nodes become visible
- Keyframes 2 → 3: Nodes remain visible
- At Keyframe 3: Nodes become hidden
- Keyframes 3 → 4: Nodes stay hidden
Typical Use Case
Let’s say you want to show the entry of a ligand into a binding pocket, but keep the receptor hidden in the beginning for clarity. You can use Flash to make the receptor appear just at the moment the ligand binds, and hide it again as the animation concludes — ensuring your audience focuses exactly where you want them to.
This gives you clean temporal control over visibility — without complicating matters by adjusting rendering styles or transparency levels.
Adding Flash to Your Animation
To add a Flash animation:
- Select the nodes (atoms, molecules, surfaces, etc.) you want to control.
- Double-click on the Flash animation effect in the Animation panel of the Animator.
- Adjust the four keyframes to determine when the node should be visible or hidden.
You can further refine the timing by modifying the Easing curve if you prefer a non-linear interpolation between keyframes. However, since visibility changes tend to be binary, this is often less relevant here than for transformations like movement or rotation.
Visualizing the Flash Effect
Below is an example of how Flash works in practice. You can see how molecular nodes pop in and out of view based on the animation timeline, making it easier to segment your story clearly without overwhelming your viewers:
To learn more about the Flash animation and how to integrate it with other effects like Pulse or Appear, visit the official documentation: documentation.samson-connect.net/users/latest/animations/flash/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.