When creating molecular animations for presentations or publications, molecular modelers often face the challenge of showing molecular structures gradually vanish—without making it look abrupt or confusing for the audience. While the classic ‘Hide’ effect can switch off visibility instantly, sometimes what you really want is a smooth fade out that better reflects transitions or interaction changes. If you’ve encountered this situation, the Disappear animation in the SAMSON platform might be exactly what you’re looking for.
The problem: Hiding is too sudden
Imagine you’re presenting a protein-ligand complex and want to show how the protein fades away to reveal the ligand interactions more clearly. Simply hiding the protein makes it blink out from one frame to the next—hardly intuitive. The Disappear animation offers a more gradual and visually informative alternative.
What is the Disappear animation?
The Disappear animation in SAMSON enables selected nodes—like structural models, visual models, meshes, and labels—to progressively become transparent over time. Rather than abruptly removing components from view, you can control how they fade away in a smooth transition.
How it works
Disappear animations operate on keyframes:
- Between keyframes 1 and 2, selected nodes remain fully opaque.
- From keyframe 2 to keyframe 3, the transparency increases gradually.
- Between keyframes 3 and 4, the nodes are fully transparent.
This structure provides precise control over the timing and progression of the fade-out effect. You can freely drag keyframes to tune the pace to your liking.
Practical example
Let’s say you’ve modeled a DNA strand wrapped around a protein, and you want to spotlight the DNA. Instead of abruptly hiding the protein, which can feel jarring, apply the Disappear animation to its structural model and let it dissolve gently. This draws attention to the DNA without confusing your audience.
How to add it
- Select the node(s) you want to make disappear. These need to support a transparency attribute.
- Double-click on the Disappear animation in the Animation panel of the Animator.
- Adjust the four keyframes to control when the transparency kicks in and how long it takes.
- Optionally, use different Easing curves to further customize the transition behavior.
Good to know
- This isn’t a blanket solution for all node types. Only nodes that support transparency can use this effect, e.g., structural or visual models—not individual atoms or bonds directly.
- If you want atoms and bonds to fade out, apply the animation to their parent structural model instead.
Conclusion
The Disappear animation is especially useful for polished presentations, where smooth transitions guide the viewer’s attention rather than forcing it. Whether you’re showing molecular interactions, structural shifts, or simply cleaning up complex visuals progressively, it’s a subtle yet impactful visual tool.
Learn more in the Disappear animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.