Have you ever needed to clearly illustrate how a ligand detaches from a receptor in a molecular complex during your presentations or simulations? Whether you’re preparing educational materials, creating a scientific demo, or simply visualizing transitions in molecular assemblies, demonstrating this type of event accurately and clearly can be challenging.
In SAMSON, the Undock animation provides an intuitive way to show molecules or meshes moving away from predefined positions—ideal for depicting the unbinding process or the transition from a docked state to a released one. Let’s explore how this feature works and how it can help clarify important molecular mechanisms.
What the Undock Animation Does
The Undock animation moves selected atoms or meshes from their initial positions (considered as docked) to final positions that are automatically computed. This method effectively simulates the movement of molecules as they dissociate from a complex. The final position is computed to ensure a clear visual separation between components, simplifying understanding for viewers.
This is particularly useful in scenarios where you need to:
- Visualize ligand unbinding
- Explain structural changes during simulations
- Present how subsystems of a molecular structure detach from a larger assembly
How to Apply the Undock Animation
Begin by selecting at least two structural nodes or meshes. Here’s the logic:
- The first node acts as the receptor (static).
- The other selected nodes are animated and move away from the receptor.
If you want multiple receptor components, just group them in a folder and select the folder first. If no selection is made beforehand, SAMSON will try to guess automatically.
Next, open the Animation panel in the Animator (use Ctrl+7 or Cmd+7 as a shortcut). Double-click on the Undock animation effect, and it will be inserted between the currently active keyframes.
You can then move keyframes as needed to change the timing of the animation. By adjusting these frames, you control when the undocking begins and how long it takes.
Controlling the Motion
The displacement amplitude is automatically computed—but if you want more control, use the Inspector to change this manually. This lets you decide how far apart the components should be at the end of the animation.
Other editable parameters include the easing curve, which modifies how your animation interpolates over time. Want a slow start and fast finish? That’s one click away.
Visual Example
Here’s what the Undock animation looks like in action. In this animation, two molecular components are initially docked together. As the animation progresses, the ligands move smoothly away from their docked positions, mimicking an unbinding event:
Why This Matters
Scientific visuals are more than just pretty animations—they help communicate complex phenomena clearly. The Undock animation allows for effective storytelling in molecular design and education. Whether you’re submitting a video abstract, giving a lecture, or creating student-friendly materials, demonstrating separation or release events has never been more accessible.
To learn more and try it yourself, visit the official documentation page.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download it here: https://www.samson-connect.net