Creating compelling molecular visualizations is an essential part of communicating molecular mechanisms, whether you’re preparing presentations, producing educational videos, or designing research figures. But there’s a frequent challenge molecular modelers face: how do you smoothly reveal or hide parts of a complex molecular structure without disrupting the viewer’s focus?
This is where SAMSON’s Disappear animation comes in. Unlike an abrupt hide function, the Disappear animation progressively increases a model’s transparency over time, letting parts of your molecular system fade out gradually. This subtlety can be a game-changer when you want your viewers to understand the spatial relationships in your model without sudden interruptions.
Why modelers use progressive disappearance
When showcasing large assemblies like proteins, polymers, or supramolecular complexes, it’s often necessary to hide components to focus on others. However, instantly hiding parts of your system can be visually jarring. Instead, a progressive fade helps maintain visual continuity, especially in animations and demonstrations.
The Disappear animation in SAMSON allows exactly that — but it works only on nodes that support transparency. This includes structural models, visual models, meshes, and labels. If you’re working with atoms or bonds directly, note that they themselves don’t have an opacity attribute; instead, apply the animation to their parent structural model.
How to apply the Disappear animation
It’s simple to use:
- Select the nodes you’d like to fade out — for example, a chain in a protein complex.
- Double-click the Disappear animation in the Animation panel of the Animator.
The animation comes with 4 keyframes:
- Keyframes 1–2: Nodes remain fully opaque.
- Keyframes 2–3: The fade begins — transparency gradually increases.
- Keyframes 3–4: Nodes become fully transparent.
You can adjust the timing and shape of the animation curve by dragging these keyframes in the timeline. For further refinement, you can also tweak the easing curve, which controls how transitions accelerate or decelerate over time.
Before you start
Be aware that older tutorials may show an outdated interface. Currently, animations are accessed via the Animation panel in the Animator, not through a top-level menu. You can open the Animator with Ctrl + 7 (or Cmd + 7 on Mac).
Fading storyboard ideas
Need inspiration on when to use fade animations?
- Gradually make side chains disappear to focus on protein backbones.
- Fade out solvent molecules to reveal core interactions.
- Use labels with fading effects to guide attention in video explanations.
To learn more, visit the full documentation page for the Disappear animation: https://documentation.samson-connect.net/users/latest/animations/disappear/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.