When presenting a molecular model, a crowded scene can make it difficult to focus attention on one part at a time. Hiding and showing nodes manually may work while exploring a structure, but it can interrupt a carefully timed explanation. SAMSON’s Flash animation offers a simple way to control when selected nodes are visible during an animation.
The key detail is that Flash changes visibility, not transparency. A node switches between hidden and visible; it does not gradually fade in or out. That distinction matters when planning a presentation: use Flash for a clear reveal or temporary disappearance, rather than for a translucent transition.
A four-keyframe visibility sequence
Flash uses four keyframes to create a timed on-and-off sequence:
- 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 stay hidden between keyframes 3 and 4.
This makes Flash useful when you want a component to be absent at first, appear for a portion of the animation, and then disappear. For example, you might use it to bring a selected molecular component into view during a particular part of a presentation, then remove it from view so attention can return to the rest of the model. The exact timing depends on where you place the keyframes.
Set it up and adjust the timing
First, choose the nodes whose visibility you want to control. Then, in the Animator’s Animation panel, double-click the Flash animation effect. Once it has been added, move its keyframes to position the hidden and visible portions of the sequence where they fit your presentation.
A helpful way to plan the timing is to decide three things before adjusting the animation: when the nodes should first be visible, how long they should remain visible, and when they should disappear. The four-keyframe sequence gives you points to arrange that visibility window. If the reveal happens too early or the nodes remain visible for too long, reposition the keyframes rather than changing the molecular structure.
Because the effect is based on visibility, it is also worth checking the sequence from the beginning and at each keyframe. That helps confirm that the nodes are hidden before the reveal, visible during the intended interval, and hidden again afterward. Flash is a presentation tool for controlling what is shown, not a way to modify the underlying molecular model.
What the easing option does—and does not mean
The animation’s easing curve can be changed to adjust how parameters are interpolated between frames. However, Flash’s visibility change is not a transparency fade: nodes switch between hidden and visible. If your goal is a gradual fade, this visibility-based behavior is not the same effect.
For a focused reveal, select the relevant nodes, add Flash, and arrange its four keyframes around the moment you want viewers to see them. You can read the Flash animation documentation for the full instructions.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.