When preparing a molecular animation, a common challenge is deciding when a structure should be visible. A component may need to stay out of view until a particular moment, appear for an interval, and then disappear. Trying to communicate that sequence with a fade can suggest gradual transparency, when what you actually need is a clear change in visibility.
SAMSON’s Flash animation is designed for this kind of on-and-off presentation. It changes whether selected nodes are visible; it does not make them transparent. That distinction is useful when you want a component to be absent, then shown as a whole, rather than gradually blended into the scene.
A timed visibility sequence
Flash uses four keyframes to define a simple sequence:
- From keyframe 1 to keyframe 2, the selected nodes stay hidden.
- At keyframe 2, they become visible and stay visible between keyframes 2 and 3.
- At keyframe 3, they become hidden and remain hidden between keyframes 3 and 4.
In practical terms, this gives you a hidden interval, a visible interval, and another hidden interval. For example, when presenting several parts of a molecular model, you can use a Flash effect to keep a chosen set of nodes out of view until the point in the animation when you want the audience to notice it. You can also use the ending hidden interval to keep that set out of the remaining sequence.
Because the effect uses visibility rather than transparency, it is not a fade-in or fade-out. If your goal is to show a structure gradually blending into the scene, Flash is not describing that behavior. If your goal is a deliberate, unmistakable switch between hidden and visible, it is a better fit.
Set it up, then adjust the timing
First, select the nodes you want the effect to control. Then, in the Animator’s Animation panel, double-click Flash to add the animation. The four keyframes establish the visibility pattern, and you can move them to adjust when the hidden and visible intervals occur.
This makes timing a useful part of the editing process. If the component appears too early, move the relevant keyframes later. If its visible interval feels too short, adjust the positions that define the interval. You do not need to change which nodes the animation targets just to revise its timing.
It can help to think about the sequence before adjusting the keys: when should the selected nodes first be visible, how long should they remain visible, and when should they disappear? Answering those questions gives you a concrete timing plan to work toward. Play back the animation after moving the keyframes to check that the visibility changes happen at the intended moments.
What the easing option does—and doesn’t mean
The Flash properties include an Easing curve, which changes how parameters are interpolated between frames. It is worth keeping this separate from the main purpose of Flash: the documented effect is based on node visibility, not transparency. So if you need a straightforward hidden-visible-hidden sequence, begin with the four-keyframe timing and use the easing setting as an additional property to explore.
Flash is most useful when the point of an animation depends on a clear reveal or removal of selected nodes. Choosing visibility changes instead of implying a fade can make the sequence easier to interpret, especially when you want viewers to focus on a particular part of the molecular model at a specific moment.
For the full instructions and property details, see the Flash animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.