When working with molecular simulations or modeling, one of the most common visualization challenges involves communicating structural dynamics effectively. There are times when entire groups of atoms, residues, or molecules should fade in and out of view to direct attention, illustrate an interaction sequence, or simply clean up a visually cluttered scene. But how can this be done without losing clarity?
This is where visibility animations in SAMSON can play a big role. In this post, we’ll focus on the Shown animation effect—what it’s for, why it’s useful, and how to add it effectively within an animation timeline.
Why use the Shown animation?
The Shown animation effect allows you to make nodes appear in the scene across a certain time interval during an animation. This is visually similar to the Appear animation, but it relies on toggling visibility directly—without using transparency or effect-based opacity transitions.
This distinction is important if you want the object to be completely absent from the rendered scene until it is needed. That helps reduce visual noise and keeps complex scenes digestible for the end viewer.
When is this especially useful?
- Highlighting a ligand binding only after the receptor has been introduced
- Bringing in interacting molecular elements one after the other during a presentation
- Building up a complex supramolecular system step-by-step for didactic purposes
How to use the Shown animation
To use the Shown animation:
- Select the molecular nodes that you want to make visible during a segment of the animation.
- Open the Animation panel within the Animator.
- Double-click on the Shown animation effect. This will create a keyframe at the current frame.
- You can drag and reposition the start and end frames to control when the nodes appear.
Note: You can always move animation keyframes later, so it’s easy to fine-tune visibility timing.
Visibility vs Transparency: Two different tools
If you want a visual emphasis without fully removing a part of the model, try using the Appear animation instead — which uses transparency and might be better for gradual transitions. In contrast, Shown leaves no trace of the object until it is fully visible, making it excellent when preparing animations for educational visuals or publications where clarity matters most.
Tuning Transition Effects
To make the transitions smoother or more dynamic, change the interpolation behavior by adjusting the easing curve of the animation. This can help, for example, if you want the appearance to feel more natural by gradually ramping in instead of switching instantly.
This animation example shows how structures can be introduced and removed, clearly illustrating a molecular event without overwhelming the viewer.
You can combine Shown with its counterpart Hidden for more complex control, such as showing a conformation at a specific point and then removing it after interaction.
To learn more about the Shown animation and additional options for visualizing molecular motion, visit the full documentation here:
https://documentation.samson-connect.net/users/latest/animations/shown/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.