When creating molecular animations, clarity is everything. Whether you’re illustrating mechanisms of action, molecular interactions, or structural rearrangements, guiding your audience’s focus without overloading the scene is a challenge. One effective way to enhance focus is by hiding parts of the structure at the right time—and SAMSON offers a simple, non-destructive way to do just that with the Hidden animation effect.
If you’ve ever been frustrated by visual clutter in your animations—ligands blocking your active site, solvent molecules interfering with a clear view of a reaction, or large biomolecular assemblies hiding critical regions—the Hidden animation is designed for you. Unlike transparency, which can still introduce visual noise, the Hidden effect completely removes objects from view between two frames without altering their properties. This provides a cleaner and better-focused narrative.
What Does “Hidden” Actually Do?
The Hidden animation makes nodes invisible between two keyframes by controlling their visibility—not by changing their transparency. This ensures that parts of your model are actually absent when you don’t need them, making the remaining components and transitions easier to understand during a presentation or in a teaching context.
When Should You Use It?
This tool is especially useful when you need to:
- Temporarily remove water molecules or solvents to highlight active binding pockets
- Show structural transitions without the distraction of supporting elements
- Switch between different focus regions within a large molecular assembly
How to Apply the Hidden Animation
Using the Hidden animation in SAMSON is straightforward and non-destructive:
- Select the nodes (atoms, residues, molecules, surfaces, etc.) you want to hide.
- In the Animation panel of the Animator, double-click the Hidden effect.
- This sets the beginning keyframe at your current frame. You can then move or adjust keyframes as needed to control exactly when the object becomes hidden and when it reappears.
Note: Keyframes can be repositioned at any time, giving you flexibility to fine-tune your animation timeline.
Combining with “Shown” for Smooth Control
The Hidden animation is often used in tandem with the Shown effect, which makes nodes visible again between two keyframes. Used together, you can precisely choreograph the entrance and exit of elements in your molecular scene.
The GIF above demonstrates how structures can be hidden and shown to focus attention dynamically. Notice how clarity improves when elements disappear at just the right moment.
Additional Tips
- Use easing curves to control the temporal interpolation and make transitions feel smoother: learn more.
- You can always revert visibility settings without losing data or having to reload your model.
Whether you’re preparing a conference presentation or teaching a class, the Hidden animation in SAMSON offers a precise, flexible solution to guide your audience’s focus and improve comprehension of molecular processes.
To learn more about the Hidden animation, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/hidden/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.