When presenting molecular systems and simulations, timing is everything. Whether you’re building educational content, preparing a presentation for a research group, or creating a guided molecular animation, there’s always one recurring challenge: how to draw attention to a specific part of a structure at just the right moment.
One effective solution in SAMSON for this kind of visual emphasis is the Flash animation. As molecular modelers increasingly share animated content, quickly revealing or hiding components in a smooth and controlled way provides clarity to the audience — especially when introducing or explaining complex molecular assemblies.
What Does the Flash Animation Do?
The Flash animation makes selected nodes (atoms, molecules, models, etc.) appear and disappear at given keyframes through visibility settings, not through partial transparency. In other words, the objects are either visible or not, which creates a clear effect similar to flipping a light switch.
This approach is particularly useful when you need a distinct cut — for example, to show only the ligand binding pocket for a few seconds, or suddenly introduce an interacting molecule right when the reaction starts without gradually fading it in or out.
How It Works
When you add a Flash animation to selected nodes using the Animation panel of the Animator, it automatically creates four keyframes:
- Keyframes 1-2: nodes hidden
- At Keyframe 2: nodes become visible
- Keyframes 2-3: nodes remain visible
- At Keyframe 3: nodes become hidden again
- Keyframes 3-4: nodes remain hidden
You can easily reposition these keyframes along your timeline to adjust when the “flash” occurs. This gives you full control over how brief or extended the appearance should be.
Use Cases for Molecular Modeling
Below are a few examples where the Flash animation proves helpful:
- Highlight a functional residue during a mechanistic animation.
- Present protein domains step-by-step, aiding understanding for students or collaborators.
- Draw attention to reaction intermediates by flashing only the atoms involved at specific steps in a catalytic cycle.
- Compare modes of action by scripting alternate molecular poses or ligands to flash sequentially.
Additional Controls
Want the transition to feel a bit more dynamic? You can adjust how node visibility changes between keyframes using the Easing curve. This allows for smoother or more abrupt timing of the visibility transitions, depending on your storytelling goal.
Conclusion
The Flash animation is a small but powerful visual tool in SAMSON that helps guide your viewer’s attention with precision. When communicating the invisible — like molecular processes — timing and clarity are everything. The Flash effect lets you selectively direct focus while keeping the rest of the scene undisturbed.
To learn more about how to use the Flash animation and other animation tools in SAMSON, visit the official documentation: 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.