When working with complex molecular systems, it’s easy to get lost in a sea of atoms, bonds, labels, and models. Whether you’re crafting a presentation for a paper or a visualization for teaching, clarity is key. One common pain point molecular modelers face is how to reduce visual clutter without removing data.
This is where the Disappear animation in the SAMSON platform comes in handy. Rather than abruptly hiding parts of your model, this animation allows you to progressively fade them out, guiding your viewer’s focus over time. It’s particularly useful for storytelling—such as revealing a binding pocket, visualizing large-to-small scale transitions, or simply cleaning up the view as something new comes into focus.
Why fading is better than hiding
You might already be familiar with the Hide animation. Disappear goes a step further: it allows nodes to transition from fully visible to fully transparent across a time range, instead of vanishing instantly. This subtle transition can help audiences better follow what’s happening in your animation or presentation.
Important: The Disappear animation only works on nodes that have a transparency attribute—such as structural models, visual models, meshes, and labels. Atoms and bonds don’t have an individual transparency attribute, but their structural model does. So if you want atoms to fade out, make sure to apply the animation to their parent model.
How to apply the Disappear animation
- Select the nodes you want to make disappear over time.
- Navigate to the Animation panel in the Animator.
- Double-click on the Disappear animation effect.
The animation consists of 4 keyframes:
- Keyframe 1 to 2: Nodes stay fully opaque.
- Keyframe 2 to 3: Nodes gradually become transparent.
- Keyframe 3 to 4: Nodes are fully transparent.
By moving the keyframes, you control when or how long each fade step occurs. Want the model visible for half the animation, then vanish quickly? Adjust the second and third keyframes accordingly.
Enhance transitions with easing curves
Sometimes a linear fade feels too mechanical. SAMSON allows you to customize the interpolation between frames using easing curves. This way, your fade can start slowly and speed up, or simulate easing in and out, giving you full control over the pacing of transparency changes.
This kind of nuanced presentation can make your molecular visualizations not only more engaging but also more informative, especially when used to direct viewer attention or signal structural transitions.
In this example animation, the Disappear effect is used alongside the Appear animation to elegantly swap between molecular views over time. Instead of getting lost in simultaneous models, the audience is guided through the content step-by-step—without overwhelming visuals.
This approach is useful in many settings: structural biology presentations, educational videos, or even internal communications where clarity of molecular structure is needed. Rather than clutter, you show sequences.
To learn more and see examples, visit the full documentation page for the Disappear animation: https://documentation.samson-connect.net/users/latest/animations/disappear/
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here: https://www.samson-connect.net.