One common challenge for molecular modelers, structural biologists, and those preparing scientific presentations is communicating movement in molecular systems. Showing how a ligand detaches from a receptor, for example, is not only useful for storytelling but also enhances understanding of molecular dynamics. If you’ve ever struggled to visually represent such undocking processes without writing custom scripts or relying on simulation data, you’re not alone.
The Undock animation in SAMSON offers a fast, intuitive solution to animate the separation of molecular components — no programming or simulation required. Here’s how you can use it to visualize undocking events simply and effectively.
Why Use the Undock Animation?
Visualizing a molecule detaching from another can be crucial. Whether you’re preparing for a lecture, sharing your work with a collaborator, or submitting a molecular video alongside a paper, animations tell stories that static images cannot.
The Undock animation displays the process of a group of atoms or meshes separating from their original, docked positions. It automatically computes new positions for the undocking process, giving you a natural-looking transition between two keyframes.
How to Apply the Undock Animation
- Start by selecting the structural nodes or meshes you want to animate. Select at least two:
- The first selection acts as the receptor (the static part).
- The subsequent selections are treated as the moving parts that will undock.
- If you want multiple static nodes to act as a single receptor, group them into a folder and select the folder first.
- Then, go to the Animation panel in the Animator.
- Double-click the Undock effect.
That’s it — SAMSON automatically computes the movement path and amplitude! The undocking happens between two keyframes, so you can fine-tune the motion just by dragging the keyframes along the timeline.
Tips for Better Control
- Want to change the amplitude of the undocking motion? Open the animation in the Inspector and adjust it manually.
- Control the timing and feel of the movement with easing curves.
- Reassign or leave selections empty: If you don’t select anything, SAMSON will guess what should be animated — a helpful shortcut, but not always exact.
This approach is especially handy if you want to depict hypothetical binding/unbinding events without running complex molecular dynamics simulations. It’s also great for educational purposes — students get to see what’s happening during molecular interactions.
See It In Action
In the example above, the ligand smoothly transitions away from its binding pocket — ideal for enhancing your molecular presentations.
Note: The older Animation menu shown in some tutorials has been replaced. You can now access all animations from the Animation panel in the Animator. Just use Ctrl+7 (Windows/Linux) or Cmd+7 (macOS) to open it.
To explore the full details of the Undock animation feature, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/undock/
SAMSON and all SAMSON Extensions are free for non-commercial use. To get started, download SAMSON at https://www.samson-connect.net.