In molecular modeling and presentations, visual clarity is crucial. Whether you’re creating an educational video, sharing research results, or simply exploring complex systems, you often need to direct the viewer’s attention to specific parts of a molecular structure. One effective way to do this is by controlling transparency — making some components gradually disappear while keeping others in focus. In the SAMSON platform, this is achieved with the Disappear animation effect.
Unlike the standard Hide function which removes elements instantly, the Disappear animation allows for a smooth transition — a fade-out effect — that can be synchronized with your scene to better convey complex molecular transformations or highlight critical structural changes. This post will guide you through how to apply this effect in SAMSON and explain when you’ll want to use it.
Why make elements disappear?
If you’ve ever tried to present a crowded molecular scene, you know how quickly it becomes overwhelming. Maybe you’re showcasing a protein-ligand interaction, and you want the viewer to focus on the binding site over time. Or maybe you’re illustrating a multi-step reaction mechanism and need to phase out intermediate structures as the reaction progresses.
This is where the Disappear animation is helpful. It lets you:
- Focus on specific atoms, residues, or domains
- Dynamically reorganize how your molecular content is revealed
- Create smoother transitions between scenes by fading structural components out instead of abruptly hiding them
How the Disappear animation works
The Disappear animation is only applicable to nodes with a transparency attribute. These include:
- Structural models
- Visual models
- Meshes
- Labels
Molecular elements like atoms and bonds do not directly support transparency; instead, their parent structural models do. So, if you want atoms and bonds to fade out, apply the animation to the entire structural model.
Step-by-step: Applying the fade-out effect
- Select the nodes you want to fade out (e.g., a structural model).
- Open the Animation panel from the Animator.
- Double-click on the Disappear effect to add it to your timeline.
This animation uses 4 keyframes:
- Keyframe 1 to 2: fully opaque
- Keyframe 2 to 3: fade-out transition begins
- Keyframe 3 to 4: fully transparent
You can move the keyframes to control when and how fast the transparency changes. Additionally, change the easing curve to modify how the fade occurs over time (e.g., linear, ease-in, ease-out).
Things to keep in mind
The Disappear animation adds sophistication to your molecular visuals, but its reach is limited to certain node types. If you’re unsure whether a component supports transparency, check if it belongs to a structural or visual model and not individual atoms or bonds.
You can always preview the animation and adjust its parameters as you go. And remember — subtle fading transitions can help your audience better understand the molecular story you’re telling, without unnecessary visual noise.
To learn more, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/disappear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.