When creating animations of molecular systems, there’s often a subtle challenge that becomes painfully clear during presentations: showing the right part of the system at the right moment. Molecular modelers regularly struggle with visual clutter that hides key mechanisms or distracts the viewer. For example, if you’re presenting a ligand binding to a protein, surrounding solvent molecules or other structural components might obscure the binding pocket at exactly the wrong time.
This is where SAMSON’s Flash animation effect can help — it lets you make parts of your molecular system appear and disappear very precisely, without resorting to opacity tricks or complicated scripting. And notably, it works based on visibility, which avoids rendering complexity and ensures clarity.
What does the ‘Flash’ animation do?
The Flash animation effect switches node visibility at specific keyframes:
- Nodes stay hidden from keyframes 1 to 2
- Nodes become visible at keyframe 2 and remain visible until keyframe 3
- Nodes become hidden again at keyframe 3, and stay hidden through keyframe 4
In short, the selected nodes “flash” into view and back out, creating a clear visual focus on specific structures or actions without relying on gradual fade-ins/outs or manipulations of alpha transparency.
This is particularly helpful in:
- Showing ligand entry and exit by toggling parts of the protein to reveal interaction sites
- Animating conformational changes where some domains briefly expose internal structures
- Highlighting symmetrical aspects of molecular complexes by alternating parts in view
How to use it
From the Animation panel in SAMSON’s Animator, you can apply the Flash effect as follows:
- Select the nodes (e.g., molecules, fragments, structural domains) you want to appear temporarily
- Double-click on the Flash animation in the list
- Adjust the timing by moving keyframes — this allows you to sync the visibility change with other animation events
The snapshot below shows how the nodes become visible and disappear again across a defined timeline:
Controlling the dynamics
The transitions between visibility states are abrupt by default, but you can influence the “feel” of the transition using easing curves. These curves let you fine-tune timing, for example making the flash-in event feel more sudden or slightly delayed relative to time markers.
By combining the Flash effect with node selection tools, camera animations, and color changes, you can communicate complex molecular events clearly — and more effectively than static images or crowded videos typically allow.
To learn more, read the full documentation page for Flash animations here: https://documentation.samson-connect.net/users/latest/animations/flash/
SAMSON and all SAMSON Extensions are free for non-commercial use. Try it for yourself at https://www.samson-connect.net.