Communicating molecular interactions doesn’t stop at showing static structures. For molecular modelers trying to convey how ligands unbind or how complex molecular assemblies disintegrate, producing clear, dynamic visualizations can become critical—especially in presentations, publications, and educational settings.
One common challenge in modeling workflows is visualizing the unbinding of a ligand from its receptor. Doing this manually, or by defining coordinates and trajectories frame-by-frame, is typically cumbersome and time-consuming.
This is where the Undock animation in SAMSON offers a major improvement. It provides an automatic way to undock parts of a molecular model—like a ligand—from their associated positions (which it assumes are “docked”). By simply selecting the molecular components and applying the Undock effect, motion is generated away from the docking site. This helps convey interaction reversals or exits efficiently.
When should you use the Undock effect?
Whenever you need to:
- Show a ligand leaving a binding pocket
- Visualize disassembly of structures like protein complexes or nanostructures
- Create simple reverse animations of docking events
- Illustrate flexibility in drug design presentations
The good news is that it’s not just a reversed Dock animation—it calculates final positions automatically, saving time and reducing the need for manual path planning.
How to apply the Undock animation
Start by selecting at least two structural nodes or meshes in your document using SAMSON’s selection tools. The first selected node acts as the receptor (static), and the other nodes will be undocked in the animation.
If your receptor group consists of multiple components (e.g., protein chains), you can place them in a folder and select the folder as the first node. If you don’t select any nodes, SAMSON tries to guess the appropriate assignments, but selecting manually gives you control over the results.
Once selected, just double-click on Undock in the Animation panel of the Animator. That’s it—the animation gets added between two keyframes. You can move these keyframes along the timeline to adjust timing.
Fine-tuning the animation
By default, SAMSON estimates an amplitude for movement—how far the undocked parts fly away. But if you need more control:
- Use the Inspector to modify the undocking amplitude.
- Adjust the easing curve to control how quickly the parts start or stop moving.
Here’s an example showing the Undock effect in action:
Note that previous versions of SAMSON had an “Animation” menu, but now all animation features, including Undock, are located inside the Animator panel—streamlining access and simplifying workflows for animators.
Who benefits from this?
If you’re a scientist preparing a conference talk, an educator explaining molecular recognition, or a researcher building interactive documentation for a ligand design project, the Undock animation helps make your messages more accessible and intuitive to your audience.
It’s especially effective to pair Undock with the Dock animation to build complete binding-unbinding cycles within one presentation. This makes it easier to represent reversible interactions such as drug docking or mechanical disassembly.
Learn more in the official SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.