When preparing molecular animations to communicate modeling results, clarity and visual progression are key. Whether you’re recording a molecular dynamics simulation or simply creating a narrated presentation for a classroom or conference, transitions help guide viewers’ attention. One transition that’s often overlooked but surprisingly powerful is a fade — and in SAMSON, this comes in the form of the Disappear animation.
This blog post walks you through how to use the Disappear animation in SAMSON to make molecular models progressively fade out rather than vanish abruptly. This small visual cue can make a big difference in how your audience follows complex visualization sequences — particularly in crowded molecular scenes. If you’ve ever struggled with cluttered models or jarring disappearances, read on.
Why fading matters in molecular visualization
Simultaneously viewing multiple molecular components — receptors, ligands, solvent molecules, visual annotations, etc. — is routine during structure analysis or when preparing videos. Often, you may want to momentarily remove elements (such as labels or secondary structures) to bring focus to others. But toggling visibility instantly can feel jarring and may briefly confuse viewers — especially in sequences where many parts appear/disappear in succession.
The Disappear animation provides a more fluid alternative by gradually increasing the transparency of selected nodes. This allows for smoother transitions and produces polished animations that are easier to follow.
What can Disappear animate?
Disappear works on any node type that supports transparency. This includes:
- Structural models
- Visual models
- Meshes (e.g. surfaces, densities)
- Labels and annotations
Note: individual atoms and bonds do not have their own transparency attributes. To control the transparency of atomic models, apply the animation to the structural model containing them.
Setting it up in SAMSON
Here’s how to apply the Disappear animation in SAMSON’s Animator panel:
- Select the nodes (e.g., models or labels) you want to fade out.
- Double-click the Disappear animation in the Animation panel.
This adds an animation with 4 keyframes:
- Keyframes 1–2: Model is fully opaque
- Keyframes 2–3: Transparency increases smoothly (model fades)
- Keyframes 3–4: Model stays fully transparent
You can move these keyframes to control the timing of each stage. For instance, you can make the fade happen quickly, or stretch it out for dramatic effect — particularly useful in storytelling contexts. You can also edit the easing curve to fine-tune how transparency changes over time — linear, exponential, etc.
A visual example
Below is an example showing both Appear and Disappear animations in action:
While the disappearing effect may seem simple, its thoughtful use can help make animations cleaner, less jarring, and more effective for guiding attention.
When to choose Disappear over Hide?
The Hide animation immediately removes the selected nodes from view. Use Hide if immediacy is needed (e.g., toggling views), but prefer Disappear when building a smooth narrative or drawing attention away gradually.
To explore further ways to enhance molecular presentations, visit the official 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 at https://www.samson-connect.net.