Setting up realistic presentations of molecular interactions often involves visualizing molecules transitioning between docked and undocked states. Whether you’re demonstrating a ligand leaving a binding pocket, or separating structural elements for clarity, precise control over these animations can make your molecular designs more compelling and easier to understand. If you’ve struggled with animating molecular dissociation effectively, SAMSON’s Undock animation may be exactly what you need.
What is the Undock Animation?
The Undock animation in SAMSON automatically creates motion for atoms or meshes that are initially in a docked state, smoothly moving them to an undocked position. This is particularly helpful for presentations, training sessions, or sharing molecular mechanisms with collaborators or students.
The Modeling Pain It Solves
A common challenge for molecular designers is showing how complex structures interact, especially when you want to visually separate components without manually adjusting every trajectory. This is where the Undock animation excels—it calculates final positions automatically, reducing the time spent on manual setup and ensuring clean, accurate visualizations of separation events.
How to Use the Undock Animation
- In your document, select at least two nodes or meshes. The first one will serve as the static reference (the docking site).
- If you want multiple nodes to act as a receptor, place them in a folder and select that folder first.
- Open the Animation panel in the Animator (shortcut: Ctrl+7 or Cmd+7 on macOS).
- Double-click the Undock animation effect to apply it.
SAMSON will move the selected nodes automatically between the two keyframes. You can adjust when the undocking happens by moving the keyframes, and customize the effect further via the Inspector.
Tuning the Animation
- Amplitude: The distance moved is set automatically, but you can manually change it via the Inspector panel to refine the visual impact of your animation.
- Easing Curve: Need a slower start or a snappier finish? Change how parameters are interpolated between frames using the Easing curve.
Visual Example
Here’s an example of the Undock animation in action:
Tips for Better Presentations
- Use undocking alongside the Dock animation to illustrate reversible processes.
- Combine with the Hold atoms animation when some parts of the molecule should remain stationary.
To learn more about the Undock animation and its use cases, visit the official documentation page: Undock Animation Documentation
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.