If you’ve ever built a scientific animation to illustrate a drug binding mechanism or a structural change in a complex protein system, you’ve likely faced this issue: how do you clearly show parts of a system disappearing to reveal what lies behind, without just fading them into transparency?
For molecular modelers and educators, being able to control what is visible in a presentation—and when—is key to directing attention. Simply modifying the transparency of molecules can leave distracting outlines or a sense of clutter. There’s a better way in the SAMSON platform: the Hidden animation effect.
What is the Hidden animation?
The Hidden animation in SAMSON toggles the visibility—not transparency—of selected nodes, such as molecules, proteins, or surfaces. Between two animation keyframes, those nodes become completely invisible, allowing you to focus on other elements of your scene. This is especially helpful in tutorials, scientific videos, or research talks where clarity matters.
For example, you might want to:
- Hide a membrane to reveal an active site.
- Temporarily remove a polymer to focus on a ligand path.
- Create transitions where elements enter or exit the scene clearly and purposefully.
How to apply the effect
Here’s how to use the Hidden animation in a few steps:
- Select the nodes you’d like to hide in your animation (e.g., a molecule, group, or custom selection).
- In the Animation panel of the Animator, double-click on the Hidden animation effect. This sets the current time as the starting keyframe.
- Move the timeline slider and adjust the end keyframe so the hiding happens where you want it.
- You can always adjust your keyframes later by dragging them directly on the timeline.
Tip: You can combine Hidden with other animation types like Shown or Flash for dynamic multi-stage presentations.
Timing and Easing
The effect can be tuned visually by editing the easing curve. This controls the speed at which the hiding happens between frames. Smooth transitions can make a presentation feel more polished and help audiences follow the motion better.
Interface note
In earlier versions of SAMSON, animations were accessed from an Animation menu. This menu has been replaced. You now access all effects—including Hidden—directly from the Animation panel in the Animator (shortcut: Ctrl + 7 or Cmd + 7 on Mac).
This animation demonstrates the combined use of the Shown and Hidden effects, letting structures appear and disappear completely for cleaner and more precise visual storytelling.
Learn more in the full documentation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.