When preparing molecular animations for scientific presentations or teaching, clarity is key. One common challenge for molecular modelers is how to draw attention to specific components of a structure at just the right moment, without overwhelming the viewer. That often means making some parts appear or disappear at precise times.
In SAMSON, the integrative platform for molecular design, the Flash animation offers a simple yet effective solution to this: you can temporarily show parts of your model when needed, and hide them afterwards — all without altering their transparency.
How Flash Animation Works
The Flash effect controls the visibility of specific nodes over time. It doesn’t use transparency to simulate disappearance; it actually toggles visibility at specified frames. This makes it more straightforward for cases where highlighting or hiding certain elements is important for storytelling or interpretation.
When you apply the Flash animation in the Animator’s Animation panel, it inserts 4 keyframes with the following behavior:
- Nodes stay hidden between keyframes 1 and 2
- At keyframe 2, nodes become visible and stay visible up to keyframe 3
- At keyframe 3, nodes are hidden again, and remain hidden up to keyframe 4
This structure is ideal for emphasizing certain molecules or components specifically between two keyframes, for example when showing the active site of an enzyme during ligand binding, or highlighting a fragment during docking.
Adding the Flash Animation
- Select the atomistic or mesoscopic nodes (e.g., ligands, protein chains, residues) you want to flash.
- Double-click on the Flash animation in the Animation panel.
- Use the Inspector to fine-tune parameters, such as easing curves, if you want smoother transitions between frames.
Keyframes can be moved to align perfectly with the timing of other effects or narration. This gives you full control over how and when structural elements appear and disappear.
Why Use Flash Instead of Appear/Disappear?
While similar to Appear or Disappear animations, Flash is particularly useful when you want a node to appear briefly and then be hidden again — all within a single effect. For example, if you’re building an educational animation showing ATP binding and then releasing, you may want to “flash” the ATP molecule during the interaction phase only.
Customizing with Easing Curves
To adjust how quickly visibility changes happen, SAMSON lets you edit the easing curve for the Flash animation. While a sudden switch might work for some situations, easing in and out can make transitions feel more natural and less abrupt, especially useful for slower-paced molecular animations.
This effect is especially helpful for presentations where you want to focus the audience’s attention momentarily on specific molecular features without cluttering the entire scene.
To learn more about the Flash animation in SAMSON, including additional options and use cases, visit the documentation page: https://documentation.samson-connect.net/users/latest/animations/flash/
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON from https://www.samson-connect.net.