Molecular modelers often need to visualize how molecules or fragments dissociate after docking — for instance, to show unbinding pathways, ligand release mechanisms, or just reverse a previous docking animation. Doing this manually, while attempting to create smooth, understandable animations, can be time-consuming and technically complex.
If you use SAMSON, there’s a way to automate this with a built-in animation feature called Undock, designed specifically to reverse docking-like interactions. Whether you’re preparing a presentation, a video for publication, or trying to better understand structural rearrangements interactively, the Undock animation makes the process intuitive.
What is the Undock Animation?
The Undock animation in SAMSON automatically moves selected nodes — typically atoms or molecular meshes — away from a docking location. This is done between two keyframes. The first selected node (or group of nodes, if wrapped in a folder) is treated as the static part (for example, a receptor or surface), while the rest are undocked around it. It simulates a gentle, controlled unbinding process — ideal for clear molecular visualizations.
Use Cases in Molecular Design
- Showcase how a ligand leaves a binding pocket.
- Visual storytelling of reversible processes.
- Better understand the role interface geometry plays during unbinding.
- Highlight the dynamic contrast between bound and unbound conformations.
How to Add the Undock Animation
1. Select nodes or meshes in the Document view. The first node you pick becomes the receptor. If you’re using multiple receptors, move them into a folder and select that folder first.
2. Open SAMSON’s Animation panel via Animator > Animation panel.
3. Double-click on the Undock animation effect. The animation automatically places keyframes and computes the amplitude of motion so that fragments clearly separate from their docked positions.
Customizing Motion
To adjust the separation distance or tuning of the animation:
- Use the Inspector to change the amplitude of the undocking movement.
- Modify the easing curve to control how motion progresses across frames (e.g. linear vs. ease-in/ease-out).
You can also move the animation keyframes freely to stretch or compress the time it takes for fragments to undock.
Visual Example
Here’s an example of the Undock animation applied to a molecular system. This kind of visual can form part of a presentation or scientific communication to enhance clarity.
A Quick Note on Compatibility
In older tutorials or videos, you may find references to the now-removed “Animation” menu. Instead, all animation effects — including Undock — are available from the Animator panel, which you can open via Ctrl + 7 (or Cmd + 7 for macOS users).
To try out live examples, SAMSON Connect provides several presentations that incorporate the Dock animation (the inverse process), such as:
Animating unbinding can be just as useful as animating binding. Once mastered, these tools eliminate the friction involved in creating clear and reproducible molecular visualizations involving dynamic interactions.
To learn more, visit the official documentation for the Undock animation here: https://documentation.samson-connect.net/users/latest/animations/undock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.