When preparing molecular animations, one common challenge is drawing attention to specific parts of a model without overwhelming the viewer with too much motion or information. Whether you’re highlighting a binding event, a structural change, or just toggling visibility for explanatory purposes, precise control of what’s shown — and when — is crucial.
That’s where the Flash animation in SAMSON can help. It allows you to seamlessly make selected molecular nodes briefly appear and then disappear during specific intervals of your animation. This can give your audience clear visual cues without interrupting the flow of the animation with excessive editing or transitions.
Why visibility – and not transparency – matters
The Flash animation works by toggling the visibility state of nodes, rather than adjusting their transparency. That may sound subtle, but it’s quite powerful: when a node is invisible, it is not just transparent – it’s gone. This helps ensure that the focus remains on other parts of the model and keeps the rendering performance high, which is especially useful for complex systems.
How Flash works
To use Flash:
- Select the nodes you want to flash (e.g., significant atoms, side chains, ligands).
- In the Animation panel of the Animator, double-click the Flash effect.
Flash automatically creates 4 keyframes:
- Keyframes 1-2: The targeted nodes remain hidden.
- Keyframe 2: Nodes become visible.
- Keyframes 2-3: Nodes stay visible.
- Keyframe 3: Nodes are hidden again, and remain so until keyframe 4.
This timing setup is ideal for things like staging: you can make a ligand flash into view to indicate its role in a binding event, then hide it again to reduce visual clutter.
When to use Flash
Molecular modelers often curate animations to tell a story. For example:
- Show the moment a pocket opens — flash the surrounding residues.
- Highlight ions as they migrate along a channel, flashing them into view at key frames.
- Introduce structural motifs transiently to avoid overwhelming beginners with full structures.
Rather than building separate animations or toggling visibility manually in each frame, Flash lets you manage these transitions efficiently.
Tip: Customize easing for smoother experience
You can further refine how the visibility transitions occur by tweaking the easing curve. This allows you to set, for instance, a smoother acceleration when flashing nodes into view, or a sharper drop-off when hiding them, offering more dramatic or natural-feeling effects depending on your scientific storytelling needs.
Bottom line: SAMSON’s Flash animation provides a lightweight yet effective method for drawing emphasis exactly when it matters. Keep your audience focused, maintain clarity, and use timed visibility to simplify complex animations.
To learn more, visit the official Flash animation documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.