When preparing a molecular presentation or creating a scientific animation, one common challenge is how to clearly convey discrete events, such as a ligand binding or a residue appearing. These events are often momentary and isolated and can easily be overlooked if not highlighted properly. This is where the Flash animation in SAMSON comes in handy.
The Flash animation effect allows you to make selected molecular nodes (e.g. atoms, groups, molecules) appear instantaneously at a specific moment and disappear just as quickly later—ideal for emphasizing short-lived biological or chemical events. Unlike adjusting transparency, Flash manipulates the visibility status of nodes, ensuring no ambiguity in what is shown or hidden.
Why does this matter?
Suppose you’re demonstrating a catalytic mechanism or spotlighting a mutation site. You want to control precisely when certain components become visible in your animation without distracting fade-ins or transitions, which can reduce visual clarity. The Flash animation gives you that pinpoint control, so that the audience sees exactly what you want them to notice—and when.
How the Flash animation works
To use the Flash effect, follow these simple steps:
- Select the molecular nodes you want to make appear and disappear.
- Double-click on the Flash animation effect in SAMSON’s Animation panel.
Once applied, the Flash animation generates four keyframes:
- Keyframes 1–2: Nodes remain hidden.
- At keyframe 2: Nodes become visible.
- Keyframes 2–3: Nodes stay visible.
- At keyframe 3: Nodes become hidden again.
- Keyframes 3–4: Nodes remain hidden.
This structure means you can flash an event onto the screen for just the right window of time, helping you highlight structural changes, binding events, or spatial transitions with exceptional clarity.
Adjusting the timing
You can always adjust your animation’s timing by dragging the keyframes on the timeline. This is especially useful if you want the flash to be very brief (like a reaction intermediate) or linger longer (perhaps to accompany voice-over explanation). Moving these keyframes gives you control over both the timing and duration of component visibility.
Smooth transitions with Easing Curves
Although Flash animations alter visibility in a binary way (on or off), you can still influence overall animation feel by adjusting the Easing curve. Easing curves define how timing functions between keyframes behave, allowing you to coordinate Flash with other animations that include movement or scaling for a more coherent visual flow.
Where it shines
The Flash effect is particularly effective in the following scenarios:
- Highlighting small molecules entering a receptor
- Signaling conformational shifts mid-simulation
- Pointing out specific residues or ions
- Directing viewer attention to mutation sites
In scientific storytelling, timing is a powerful way to draw attention and communicate importance. The Flash animation gives you a simple but effective way to integrate visual cues into your molecular animations to support your narrative.
To learn more and see the original documentation, visit this page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.