One common challenge in molecular modeling is presenting how a ligand exits a binding pocket or how molecular components detach over time. Whether for a presentation, a publication, or to explain a concept to collaborators, animating these motions clearly can make a significant difference in communication.
This is where the Undock animation in SAMSON becomes particularly useful. This animation effect allows you to visually separate selected groups of atoms or meshes from their current ‘docked’ positions to new locations, computed automatically to avoid overlaps. The motion clearly mimics the process of molecules unbinding or drifting apart, which can be highly illustrative in presentations and teaching materials.
Why use Undock?
In many scenarios, you might need to:
- Demonstrate separation between molecular components (e.g., receptor-ligand unbinding)
- Transition from a bound to an unbound conformation in animations
- Clarify structural relationships that are otherwise hidden due to proximity
The Undock animation simplifies this process by determining appropriate final positions and generating transitions accordingly.
How to apply it effectively
To apply an Undock animation, you first need to select at least two nodes or meshes in your molecular model. The first selection will act as the anchor (e.g., a receptor), and the second (or more) selections will be animated (e.g., the ligands or domains that move).
If the receptor consists of multiple nodes, group them into a folder and make the folder your first selection. This ensures consistency in identifying what stays put versus what moves.
Once your selections are in place, simply double-click the Undock animation effect in the Animation panel of the Animator. Keyframes will be automatically created, and motion paths will be computed for the undocking effect.
Customize the motion
The distance and direction of the motion are based on automatic computations but can be tuned. You can:
- Inspect the animation to adjust the amplitude
- Tweak keyframes to stretch out or speed up the animation
- Edit the easing curves for smoother or more dramatic transitions
These adjustments help you tailor the animation to fit your explanatory or visual goals perfectly.
A note on interface changes
If you’ve used older versions of SAMSON and recall applying animations from the Animation menu, note that animations are now accessed directly through the Animator’s Animation panel, using the shortcut Ctrl+7 (or Cmd+7 on macOS).
Visual example
The following animation shows a typical undocking motion as performed in SAMSON:
Perfect for storytelling
The Undock animation is ideal when you’re building presentation slides or video outputs that show dynamic system transitions. Combined with other effects like Dock or Move atoms, it gives you full creative control for crafting molecular stories.
To learn more: Undock Animation Documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.