When preparing molecular animations, one challenge often faced by modelers is how to clearly convey structural changes without cluttering the scene. Sometimes, the best way to highlight what’s important is to temporarily hide what’s not.
The Hidden animation in SAMSON is designed for precisely this purpose. It makes selected nodes (molecules, atoms, groups, etc.) disappear between two keyframes—not by making them transparent, but by setting them to be truly invisible.
Why hide instead of fade?
There are different ways to visually remove parts of your model in animations. Transparency is one approach, but it often leaves visual noise—objects still occupy visual space faintly. Hiding nodes, on the other hand, removes them completely from the scene, making it easier to focus viewer attention where it matters most.
How it works
Using the Hidden animation is simple and flexible:
- Select the nodes you want to hide during part of the animation. These can be any type of node—for example, a residue, an entire molecule, or just a specific atom group.
- Go to the Animation panel within the Animator interface.
- Double-click on the Hidden animation effect. A begin keyframe will be set at the current frame.
- Move forward in the animation timeline and adjust the position of the end keyframe (drag or use the timeline editor).
Once applied, SAMSON will automatically make the selected nodes invisible between the two keyframes. You can always modify keyframe positions later to fine-tune the timing.
Use case: Emphasizing changes in a reaction
Imagine you’re presenting an animation of a catalytic process. Between transition states, large portions of the system—such as solvent molecules or even cofactors—might momentarily distract from the chemical transformation. By applying the Hidden effect, you can remove these elements temporarily and direct the audience’s attention to the atoms involved in the reaction mechanism.
Hidden vs. Shown: A powerful combination
The Hidden animation pairs well with the Shown animation. While Hidden makes nodes disappear, Shown makes them reappear. Together, they let you toggle parts of your model on and off at different parts of your animation sequence. This enables step-by-step reveals of molecular assembly, folding, docking, or even results from a simulation.
Make it smoother
You can refine how the invisibility effect starts and ends by modifying the Easing curve. This lets you control whether the disappearance happens instantly or gradually over a defined number of frames, giving more natural pacing to the visual transition.
Where to find it
All animation effects, including Hidden, are available via the Animation panel in the Animator interface. The old Animation menu is no longer present, so the panel is your go-to place for accessing these effects (shortcut Ctrl+7 on Windows or Cmd+7 on macOS).
Learn more in the full documentation for the Hidden animation effect here: Hidden Animation Documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.