Presenting molecular systems often involves more than just accurate modeling. Whether you’re preparing a scientific talk, recording a video tutorial, or simply exploring different stages of a simulation, visual clarity is essential. As complexity increases, showing every fragment in your model can lead to clutter and make it harder for your audience (or even yourself) to focus on what matters most.
Enter the Hide animation in SAMSON: a simple yet powerful tool to control visibility in molecular scenes over time. This blog post walks you through how it helps molecular modelers structure cleaner narratives and presentations.
Why hide anything?
There are many reasons why molecular scientists might want to hide elements in a model:
- To reduce visual noise and focus attention on key functional groups or regions
- To progressively reveal parts of a molecular process or assembly mechanism
- To simplify reactions or interactions over time in a simulation
While you could remove components manually, using animations is much more effective—especially when creating a timeline or recording a video.
How the Hide animation works
The Hide animation is designed to make selected nodes disappear at a defined keyframe and stay hidden until the animation ends. This is achieved by switching the visibility state rather than adjusting transparency, which helps keep rendering performance high while maintaining semantic clarity in your presentation.
It’s essentially a combination of two other animations—Shown and Hidden—in one transition. It’s fast to apply and easy to manipulate.
Step-by-step: using Hide in SAMSON
- Select the nodes you wish to hide (atoms, groups, molecules…).
- Open the Animator and in the Animation panel, double-click the Hide effect.
- This creates three keyframes:
- Keyframe 1–2: nodes remain visible.
- Keyframe 2: nodes disappear.
- Keyframe 2–3: nodes remain hidden.
- Move these keyframes as needed to control the timing of the disappearance.
Tips for smooth visuals
Unlike transparency-based hiding (which may still show outlines or occluded objects), toggling visibility guarantees a clean disappearance. For dynamic presentations, try combining Hide with Appear or Flash for engaging storytelling.
If you want smoother transitions, consider adjusting the easing curve for each keyframe jump. Just remember: easing here only affects timing interpolation and won’t create a fade effect for visibility changes.
One caveat
The video shown in the documentation uses an older version of the interface. While the Animation menu no longer exists, all animations are now available through the Animator’s Animation panel (Ctrl+7 or Cmd+7).
This seemingly small feature can dramatically improve the quality and clarity of molecular presentations. It’s especially useful when working with audiences unfamiliar with complex structural biology visualizations.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/hide/
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.