Visual storytelling is powerful in science. Whether you’re preparing a presentation, recording a molecular event, or teaching a concept, the way components appear in your molecular model matters. If you’re working with molecular scenes in SAMSON, you might already know that animating parts of your model to show or hide can bring clarity and focus. But there’s a difference many users overlook — and it affects both the visual appeal and the scientific clarity of your animations.
The Shown animation in SAMSON addresses a subtle but important challenge: making nodes (atoms, residues, molecules, etc.) truly appear on screen using visibility transitions — not transparency switches. This seemingly small detail matters when you want unambiguous frames in your video, or clear on/off presence of molecular groups, without the fading ambiguities of partial opacities.
Why not just use transparency?
Transparency is useful when visualizing overlapping structures or focusing on specific spatial arrangements. However, when transparency is animated, it can cause confusion: is the node still part of the scene or is it disappearing? Is it just faint, or truly gone? If you’re preparing educational content or need to underscore steps in a process (e.g. ligand binding or catalysis), such ambiguities matter.
The Shown animation avoids this. Instead of varying opacity, it makes nodes fully invisible or visible by changing their visibility via keyframe animation. This is particularly useful when you want molecular structures to appear discreetly and decisively at specific time points.
How to use the Shown animation
To create a Shown animation:
- Select the nodes you want to animate (e.g., a protein domain or a ligand).
- Open the Animator in SAMSON and go to the Animation panel.
- Double-click on the Shown animation effect. A start keyframe will automatically be added at your current timeline position.
- Move your timeline cursor to the desired frame, then adjust your keyframes accordingly. This defines when the node appears in the animation.
All of this is accomplished without transparency effects, resulting in more intuitive and focused visual output.
Who benefits?
- Researchers making videos of protein conformational changes
- Teachers explaining molecular events like docking or electron transfer
- Students preparing visuals for class projects or presentations
You still have control over how the animation plays out over time. You can customize how the animation interpolates between keyframes by adjusting the easing curve—giving more natural-looking motion if desired.
Visual example
Here’s an animation where a group of molecular nodes becomes visible and then hidden, illustrating the crispness of appearance and disappearance using visibility — not transparency:
If you’re exploring molecular change, tracking interactions, or making your story visually clear, the Shown animation is a useful and clean solution for toggling parts of your system on and off.
To learn more, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/shown/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.