When sharing molecular animations, it can be hard to clearly indicate when specific atoms or groups appear or disappear. Whether you’re showing a ligand binding event, a reaction intermediate forming, or toggling between two conformational states, your visual message can easily become lost if transitions are too subtle or ambiguous.
This is where the Flash animation effect in SAMSON comes in handy. Instead of relying on gradual transparency or movement, Flash uses visibility toggling to make selected nodes appear and disappear at key moments. It’s a useful tool when you need to clearly say: “this group is now present” or “this part is no longer in this state.”
What is Flash animation and when to use it
The Flash animation is not about glowing effects or blinking lights — it’s a visibility toggle tool that helps emphasize scenes where elements in your molecular system suddenly become relevant or irrelevant. This is not done via adjusting transparency, but by setting node visibility states at specific keyframes.
This can be especially useful when you:
- Want to clearly show a molecule entering or leaving a binding pocket
- Need to highlight temporary states during a docking or simulation trajectory
- Present alternate binding poses or conformers without confusion
- Visually narrate mechanisms showing only key fragments step-by-step
How it works in SAMSON
To apply the Flash animation:
- Select the nodes (atoms, molecules, groups) you want to toggle.
- Double-click on the Flash animation effect in the Animation panel of the Animator.
- The Flash animation includes four keyframes by default:
- Between keyframes 1 and 2: nodes are hidden
- At keyframe 2: nodes become visible
- Between keyframes 2 and 3: nodes remain visible
- At keyframe 3: nodes become hidden again
You can move these keyframes to time the appearance or disappearance exactly how you want.
Tuning the transition with an easing curve
Although the Flash is an on/off toggle, you can still control how the transition flows using an easing curve. This adjustment defines how parameters (in this case, visibility) transition between keyframes. For instance, aligning the Flash with another continuous animation can help sync structural motions and node visibility.
Why this small feature is worth remembering
Subtle visualization challenges can have big impacts when communicating complex molecular mechanisms. Flash is one of those simple tools that helps reduce cognitive load for your viewers by making key visual points unambiguous. Whether used to punctuate a binding event or emphasize a mechanism step, Flash helps your molecular story come across more clearly.
Paired with other animation effects in SAMSON — such as Appear, Disappear, Pulse, Hide and Show — this little feature makes your scientific visuals more engaging and informative.
Learn more in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.