When preparing molecular animations for presentations or educational content, it’s often necessary to emphasize specific parts of a system only for a short duration. Whether it’s highlighting a binding site, showing ligand entrance, or drawing attention to transient structures, controlling visibility is key.
This is where the Flash animation in SAMSON can help. It’s a simple but effective way to make nodes—like individual atoms, molecules, or entire molecular groups—briefly appear and then disappear in an animation timeline. It’s different from using transparency: the Flash animation switches node visibility directly, removing them entirely from view when needed.
Why does this matter?
In scientific visualization, attention control is crucial. Suppose you’re animating a reaction mechanism or a docking process. You might want to spotlight water molecules entering or exiting a binding pocket, or quickly show residues involved in hydrogen bonding. Using Flash, you can synchronize visibility with events in your animation—without permanently cluttering the scene.
How Flash works in SAMSON
The Flash animation is added via the Animation panel in the Animator. First, select the nodes you want to appear and disappear. Then double-click on the “Flash” effect. This inserts a four-keyframe animation in your timeline:
- Between keyframes 1 and 2: nodes stay hidden
- At keyframe 2: nodes become visible
- Between keyframes 2 and 3: nodes stay visible
- At keyframe 3: nodes become hidden again
- Between keyframes 3 and 4: nodes remain hidden
You can move these keyframes to control precisely when your specified parts appear and disappear. This gives you timing flexibility and lets you align the visibility with events such as the arrival of a ligand or a conformational shift.
Bonus: Easing Curves for Transitions
While the Flash animation affects visibility rather than transparency, you can still adjust how transitions behave using SAMSON’s Easing curves. These define how parameters evolve between keyframes—even in visibility changes—offering smoother or more staggered timing feel to entries/exits when combined with other animated properties.
When to use Flash
The Flash tool is particularly helpful when:
- You want to emphasize a group only briefly in an animation
- You need to reduce screen clutter but still communicate presence
- You are sequencing different groups in an explanatory animation
It complements other visibility effects in SAMSON like Appear, Disappear, Hide, or Show. But Flash is the go-to when timing is tight and visibility needs to be coordinated precisely within the animation structure.
To learn more or try it yourself, visit the full documentation for Flash animation at this link.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.