A molecular animation can become difficult to follow when every structure is visible at once. A ligand, residue, or other selected part of a model may be important for just one moment—but leaving it on screen throughout the presentation can distract from the point you are trying to make. The Flash animation offers a simple way to control when selected nodes are visible.
Flash changes node visibility, rather than transparency. In practical terms, the selected nodes are shown or hidden; the effect is not a transparency-based fade. This distinction matters when you want a structure to be absent from the scene for part of the animation, rather than merely less opaque.
Use a brief appearance to focus attention
Imagine presenting a protein and wanting to reveal a particular group only when you begin discussing it. Instead of keeping that group visible from the start, select the nodes you want to control and add Flash from the Animation panel in the Animator. The animation has four keyframes:
- Between keyframes 1 and 2, the selected nodes are hidden.
- At keyframe 2, they become visible and remain visible between keyframes 2 and 3.
- At keyframe 3, they become hidden again and remain hidden between keyframes 3 and 4.
This gives you a contained visibility window: the nodes are hidden before the reveal, visible for the middle portion, and hidden afterward. That can help keep a presentation uncluttered while still allowing you to bring attention to a specific part of a molecular model when it is relevant.
Plan the timing around your explanation
After adding the effect, move its keyframes to fit the timing of your animation. For example, place the reveal so it coincides with the moment you want viewers to notice the selected nodes, then place the hide keyframe after that part of the explanation. The keyframes are movable, so you can adjust the visible interval as your presentation takes shape.
A useful way to check the result is to review the animation around each keyframe: confirm that the nodes are hidden before the reveal, visible for the intended section, and hidden again afterward. If the reveal or disappearance happens at an awkward point, adjust the keyframe positions rather than changing which nodes you selected.
Check the animation properties
The Flash properties include an Easing curve, which lets you change how parameters are interpolated between frames. If you are adjusting the animation, you can inspect this option in the Inspector. Flash itself is based on node visibility, so do not treat it as a transparency fade; use it when the desired result is to show and hide nodes.
Flash is especially useful when a model contains more detail than viewers need to see all at once. By limiting a selected group to the portion of the animation where it matters, you can make the sequence easier to follow without changing the molecular structure itself.
Learn more about the Flash animation in the SAMSON documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.