Switching Off Without Fading: How to Hide Molecular Components in Animations

Controlling the visibility of components in molecular animations can be crucial, especially when you’re trying to focus your viewer’s attention on specific parts of a system. But what if you don’t want a fade or opacity shift — you just want certain elements to disappear cleanly at a specific point in time? The Hidden animation in the SAMSON platform solves this exact problem.

This is especially helpful when creating molecular visualizations for presentations or videos, where clarity often matters more than gradual transitions. Rather than adjusting transparency — which can introduce visual noise — the Hidden animation effect ensures that selected objects become completely invisible between keyframes, using direct visibility settings of nodes.

When Would You Use Hidden Animations?

If you need to:

  • Clean the scene of spectator molecules to zoom in on a reaction center
  • Remove solvent shells abruptly for schematic transitions
  • Show dynamic structural rearrangements by toggling components on and off
  • Time molecular events with narration or labels that rely on quick cut-offs

…then Hidden is your tool.

How to Use It

The process is minimal and quick:

  1. Select the nodes (e.g. atoms, residues, models) you want to hide.
  2. Open the Animation panel in the Animator.
  3. Double-click the Hidden animation effect.
  4. A keyframe will automatically be added at the current frame. Move it around in the timeline as needed.

This hides the selected nodes completely between the chosen keyframes—just like switching off a light.

Example: the Shown and Hidden animations

Advanced Tips

  • You can easily mix and match this with the Shown animation for toggling visibility through time.
  • Use Easing curves to control how quickly or slowly the animation transitions between keyframes (though visibility here is an on/off logic).
  • Use multiple keyframes for fine-tuned control over when objects appear and disappear in the timeline.

Note: the legacy Animation menu shown in older tutorials is no longer present. For full control, rely on the Animation panel under Animator instead. You can access it via the interface or using Ctrl + 7 / Cmd + 7.

For more detailed instructions and related effects (Appear, Disappear, Flash, etc.), consult the full Hidden animation documentation.

SAMSON and all SAMSON Extensions are free for non-commercial use. You can download the platform and explore more features at samson-connect.net.

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