Struggling with presenting complex molecular scenes in a clean, digestible way? If you often build animations to showcase conformational changes, protein-ligand interactions, or intricate visualizations involving multiple overlapping layers, you’ve probably asked yourself: How do I control what’s visible and when?
Turning parts of your molecular model on and off is often not ideal. Sharp disappearances can feel abrupt and confusing. Fortunately, the Disappear animation in SAMSON provides a simple way to control visibility with smooth transitions, helping viewers focus on your message without distractions. ✨
The problem: Abrupt transitions in molecular animations
In integrative molecular modeling, managing the visibility of elements such as proteins, ligands, surfaces, meshes, and labels can be tricky. For example:
- You want to gradually reveal the binding pocket of a protein by fading out the surface.
- You want to move from a complete cell model to a focused subunit without sudden “jumps” in the visualization.
- You want to reduce visual clutter in presentations and videos without deleting or completely hiding objects.
The Disappear animation effect gives you a fine degree of control over this. It works by progressively increasing the transparency of selected nodes over time. The transition is smooth, giving your animation a more polished and professional feel.
When to use Disappear
The Disappear animation is perfect for nodes that support transparency attributes. These include:
- Structural models
- Visual models
- Meshes
- Labels
This means you can’t apply it directly to individual atoms or bonds, but you can apply it to the structural model they belong to. Think of it as “fading out” an entire group of atoms, rather than turning them completely off.
How it works
To apply the effect:
- Select the nodes you want to fade out.
- Open the Animator and double-click the Disappear effect in the Animation panel.
- Four keyframes are created automatically:
- Keyframes 1–2: fully opaque
- Keyframes 2–3: progressive disappearance
- Keyframes 3–4: fully transparent
- Move the keyframes to control when the transition begins and ends.
You can also modify how the change occurs using easing curves to create more natural or stylized transitions.
Useful tips
- The animation only works if the node supports transparency. If you get confused about why something isn’t fading out, check if it has a transparency attribute first.
- Want a reverse effect? Use the Appear animation, which performs the opposite action.
- You can combine Disappear with cameras, lighting changes, or labels to create well-timed stories in molecular presentations.
Here’s an example of the Disappear animation in action:
To learn more about how to use the Disappear animation and see all animation options, visit the full documentation here: 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.