When presenting a molecular model, timing matters. You may want a ligand, residue, or other selected part of a structure to appear only when you discuss it, then disappear before moving to the next point. If you rely on transparency for this, the result can be harder to manage: the object is still present but merely see-through. SAMSON’s Flash animation offers a direct alternative by changing node visibility.
Flash is useful when the goal is a clear, timed reveal or removal of selected nodes in an animation. Its key distinction is that it works through visibility, not transparency. That makes it suitable for presentation sequences where you want a component to be either shown or hidden, rather than gradually faded.
Build a simple reveal sequence
Start by choosing the nodes you want the animation to affect. Then, in the Animator’s Animation panel, double-click Flash to add the effect. Selecting the intended nodes first is important: it defines which parts of the model will flash, while other nodes remain outside the animation’s scope.
Flash uses four keyframes. The documented sequence is:
- Between keyframes 1 and 2: the specified nodes stay hidden.
- At keyframe 2: they become visible, and remain visible between keyframes 2 and 3.
- At keyframe 3: they become hidden, and remain hidden between keyframes 3 and 4.
In practice, this gives you a defined visible interval: the selected part is hidden before its reveal, shown for a portion of the animation, and hidden again afterward. You can move the animation’s keyframes to adjust when those changes happen in your presentation.
Use visibility deliberately
A useful way to plan a Flash animation is to decide what the audience should be looking at during each segment. For example, you could keep a selected set of nodes hidden while introducing the overall model, reveal them at the point where they become relevant, and hide them again before the next section. This keeps attention on the part being discussed without requiring you to alter the nodes’ transparency.
Because the animation acts on the nodes you select, consider the scope before adding it. If you want several parts to appear together, select the nodes that belong in that reveal. If a node should remain visible throughout, leave it out of the selection. This simple check can help prevent an animation from hiding more—or less—of the model than intended.
Adjust timing and interpolation
After adding Flash, move its keyframes as needed to fit the pace of your explanation. The keyframes determine when the hidden and visible portions occur, so reviewing their placement alongside the rest of the animation can make the sequence easier to follow.
You can also change how parameters are interpolated between frames by modifying the animation’s Easing curve. The Flash effect itself is based on visibility changes at keyframes; the easing setting is an additional animation property to explore when adjusting how parameters are interpolated.
A quick planning checklist
- Choose the exact nodes to show and hide.
- Add Flash from the Animator’s Animation panel.
- Check the hidden interval before keyframe 2 and the visible interval between keyframes 2 and 3.
- Move keyframes to match the pace of your presentation.
- Preview the sequence and confirm that the selected nodes—not unrelated parts of the model—change visibility.
For the full instructions, see the Flash animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.