Have you ever struggled to clearly communicate a molecular mechanism or structural change during a presentation or video? For molecular modelers and educators, timing when parts of a molecule appear or disappear can make the difference between confusion and clarity. That’s where the Flash animation in SAMSON becomes a useful tool.
The Flash animation is a visual effect that lets you control when molecular objects go from invisible to visible and back — with precision, and without relying on transparency. This can be especially useful when you’re teaching or presenting how a ligand binds to a pocket, illustrating the sequential assembly of a complex, or simply emphasizing a specific region at the right moment in your animation.
What is the Flash animation?
Unlike other visibility-based effects in SAMSON, such as “Appear” or “Disappear,” which permanently show or hide objects over time, the Flash effect is punctual: nodes (molecular structures, groups, etc.) are invisible at the start and end, and become visible only for a defined duration in-between. This creates a brief highlight for the selected objects — like a spotlight in a theater play.
How it works
When you select a group of nodes and apply the Flash effect from SAMSON’s Animator panel, it automatically creates four keyframes:
- Keyframes 1-2: the selected nodes are hidden
- At Keyframe 2: the nodes appear
- Keyframes 2-3: the nodes stay visible
- At Keyframe 3: the nodes disappear
- Keyframes 3-4: the nodes stay hidden
You can then move these keyframes in time to precisely control when your selected part of the model appears and disappears. This lets you create interruptions, pulses, or emphasis moments with minimal setup.
Use cases for better storytelling
Here are a few common situations where Flash can improve your scientific communication:
- Highlighting key residues: briefly show a catalytic triad or binding-site residues while explaining their function.
- Mechanism snapshots: draw attention to a molecule or structural domain only at the step where it interacts or changes.
- Cognitive relief: remove surrounding detail and show just one part of a complex to help your audience focus momentarily.
In short, Flash empowers you to tell better molecular stories without cluttering the screen too long with too much information.
Refining your animation
Don’t forget you can also fine-tune the timing of transitions by adjusting the Easing curve, available in the Inspector panel. This controls how smoothly your model fades in and out.
To learn more or follow detailed steps, visit the official documentation page here: https://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.