When preparing scientific animations to illustrate molecular processes, timing is everything. Whether you’re presenting a protein folding event or the binding of a ligand at an active site, getting your visuals to clearly communicate temporal changes is essential. One common pain point for molecular modelers is controlling the appearance and disappearance of components at just the right moment — without overloading the viewer with too much visual information at once.
That’s where the Flash animation in SAMSON comes in handy. This simple but effective animation lets you make selected molecular nodes become visible at one point in time and disappear at another, creating a clear visual cue for dynamic events in your molecular story.
Why use the Flash animation?
Flash is designed specifically for showing sudden, time-controlled visibility changes of molecular objects (called nodes in SAMSON). The mechanism is based on toggling visibility, rather than slowly fading objects in or out, making it ideal for demonstrating binary events, like switching between molecular states, appearance of a ligand, or highlighting an intermediate structure in a reaction pathway.
How does it work?
You can find the Flash animation in the Animation panel of the Animator. Applying it is straightforward:
- Select the nodes you wish to animate (e.g., a specific chain, a ligand, or an active site residue).
- Double-click the Flash animation effect in the Animation panel.
Once applied, you’ll see four keyframes in the animation timeline:
- Between keyframes 1 and 2: the nodes are hidden.
- At keyframe 2: the nodes become visible.
- Between keyframes 2 and 3: the nodes stay visible.
- At keyframe 3: the nodes become hidden again (and remain hidden until keyframe 4).
This makes it ideal for showing transient features — for instance, you can flash a cofactor into view during a catalytic event, and hide it again once the step is over.
Customizing timing and transitions
You’re not locked into the default timeline. All keyframes can be repositioned along the timeline to adapt the animation to your narrative flow. For example, delaying the start of the visibility or prolonging the duration of the visible state is as easy as dragging keyframes into place.
Additionally, the Flash animation supports easing curves. This allows you to tweak how interpolation occurs around keyframes, even though visibility itself is binary. Access this via the Inspector and modify easing for smoother transitions between animations (when combined with other effects).
When should you use Flash over other animations?
Although similar in name to animations like Appear, Disappear, or Pulse, Flash stands out due to its minimalism. It doesn’t involve transparency fades or multiple repeated cycles — just one clean in-and-out visibility toggle. It’s excellent for marking events like ion entry, channel opening, or highlighting residues of interest in an analysis snapshot.
To learn more about how to use Flash animation in your molecular designs, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.