It’s a common challenge for molecular modelers building scientific animations: how to present complex molecular mechanisms while ensuring the viewer’s attention is focused on the right parts—at the right time. Whether you’re illustrating ligand binding or signaling cascades, controlling when elements appear and disappear in an animation is key to clarity and impact.
This is where SAMSON’s Flash animation comes in. While transparency or color changes can signal activity, there’s something much more direct and visually impactful about making components blink in and out of view precisely when needed. The Flash animation does exactly that: it lets you show and hide molecular nodes cleanly and predictably throughout your animation timeline.
What does the Flash animation do?
The Flash animation effect in SAMSON allows selected elements—referred to as nodes—to become visible at one point in time and then disappear later, without using transparency tricks. Rather, the visibility property of each node is modified.
This makes Flash ideal for emphasizing a molecular group or residue during a specific phase of the animation. For example, you might want a ligand to flash into view as a receptor changes conformation, then disappear after binding is complete. Flash offers precision and full control over this process via an easy-to-use interface.
How it works
Here’s how you use the Flash animation in your project:
- Select the nodes you want to appear and disappear.
- Double-click the Flash effect from the Animation panel in the Animator.
Once added, the Flash animation includes four keyframes to structure visibility:
- Keyframes 1–2: the nodes stay hidden
- Keyframe 2: the nodes become visible
- Keyframes 2–3: the nodes stay visible
- Keyframe 3: the nodes become hidden again
- Keyframes 3–4: the nodes stay hidden
You can then move the keyframes to fit the timing of your animation sequence. Whether you want a momentary flash or a sustained visibility period is completely up to you.
Fine-tuning your animation
To refine the visual transitions of the Flash effect, you can adjust the Easing curve. This affects the rate of change between keyframes. While Flash is about visibility (not transparency), easing can help you synchronize flashes with other animations that do use interpolation, such as molecular movements or pulses.
Visual example
Here’s an example of how the Flash animation looks when executed in SAMSON:
This visual clarity is critical for presentations, publications, or educational videos that need to focus attention without introducing visual clutter.
When should I use Flash?
Use the Flash animation technique when:
- You want to introduce a component only temporarily (e.g., to reveal a cofactor or substrate mid-animation)
- You need to alternate between different conformations of a complex
- You want to simplify busy molecular scenes by cycling focus on key features
- You’d like your audience to interpret the sequence of events without distraction
Flash isn’t about sparkle—it’s about focus. It helps your animation tell a clearer story.
To learn more and try it yourself in your next scientific animation, visit the official documentation page for the Flash animation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.