When presenting complex molecular systems, clarity is key. Whether you’re building an educational presentation, highlighting dynamic molecular processes, or preparing figures for a talk or publication, how and when you show specific molecular components can change how your message is received.
The Flash animation in SAMSON is a helpful tool that addresses a common pain: controlling the visibility of molecular nodes with accuracy and timing — without relying on transparency tricks.
What Does Flash Actually Do?
The Flash effect toggles the visibility of selected nodes (atoms, molecules, structures, etc.) to make them appear and disappear between keyframes. Unlike transparency-based methods that can be visually subtle or ambiguous, Flash provides a clean show/hide mechanism through visibility control.
This is essential when:
- You want an atom or complex to appear precisely at a given moment in your animation sequence.
- You need to hide supporting structures before switching the viewer’s attention to another area.
- You want to spotlight a reaction intermediate, docking result, or specific feature without distractions.
How the Flash Effect Works
The Flash animation comes with four keyframes:
- Keyframe 1 → Keyframe 2: Nodes remain hidden.
- At Keyframe 2: Nodes become visible.
- Keyframe 2 → Keyframe 3: Nodes remain visible.
- At Keyframe 3: Nodes are hidden again.
- Keyframe 3 → Keyframe 4: Nodes stay hidden.
You have full control over the timing by repositioning these keyframes. This makes it easy to align appearances or disappearances with other animation events.
Applying a Flash Animation: A Quick Guide
- Select the nodes you want to show/hide (e.g., a ligand or protein domain).
- In the Animation panel of the Animator, double-click the Flash effect.
- This creates the four keyframes above. You can now adjust these along the timeline to fit your presentation flow.
- For smoother transitions, customize the Easing curve in the Inspector.
Why Not Just Use Transparency?
Transparency can be a useful tool in molecular visualization, but it presents a problem in presentations: partially transparent objects may still distract or obscure key information. Flash reverses that logic — it removes visual clutter entirely when needed and makes structure transitions more readable for your audience.
When to Use Flash
Use it when:
- Comparing large structural states (e.g., protein open vs. closed conformations).
- Revealing a ligand only during docking or binding steps.
- Cleaning up a scene by removing context molecules before focusing elsewhere.
By using visibility instead of gradual transparency, Flash helps keep animations direct, simple, and easy to follow.
Learn more about the Flash animation in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.