When preparing molecular presentations or animations, one common challenge for modelers is clearly visualizing the undocking process—how a molecule moves away from a receptor without manually animating every step. Whether you’re demonstrating binding site dynamics or highlighting changes upon inhibitor release, conveying this motion cleanly can save time and improve clarity.
SAMSON’s Undock animation effect helps solve this by automatically computing a smooth molecular unbinding path from a docked position. This functionality, built into the Animator, simplifies what would otherwise be a time-consuming process of manually planning an atom-by-atom exit path.
How it works
The Undock animation works by taking groups of atoms or meshes (e.g. a ligand or surface cluster) and moving them automatically away from their current docked positions. This is done between two animation keyframes that you place on the timeline in the Animator.
To apply it:
- Select at least two structural nodes or meshes: the first will act as the receptor, and the others will move relative to it.
- If you want multiple nodes to play the receptor role, place them into a folder and select the folder first.
- Then, in the Animation panel, double-click the Undock effect.
- SAMSON computes the undock animation automatically between the current keyframes. You can adjust these keyframes freely.
This means that you don’t need to calculate a path or program a transformation. Using the automatic behavior reduces setup steps, especially for quick iterations or educational videos. You can still fine-tune movement amplitude or easing to match your narrative.
Customizing the effect
The Undock animation starts with a predefined movement amplitude, but you can change this easily using the Inspector. A higher amplitude means elements will move further from the receptor.
You can also define how the animation behaves between the keyframes using an easing curve. This is helpful when you want smooth acceleration away from the receptor—e.g. to simulate a release mechanism—or a more mechanical constant-speed motion for engineered systems.
When to use it
The Undock animation is useful in:
- Presenting ligand unbinding in protein-ligand complexes
- Annotating how a surface pocket opens and releases a molecule
- Educational visuals for classes or talks about molecular recognition
- Creating molecular dynamics storyboard-style visuals
What it looks like
Here’s how the Undock animation effect plays out in a visual sequence:
Try it yourself
The Undock effect is one of several animation utilities available inside SAMSON. It’s compatible with features like Dock, Hold atoms, and Move atoms. Together, they offer a system for building lightweight molecular animations with minimal manual setup.
You can learn more and find related examples at the official documentation page: https://documentation.samson-connect.net/users/latest/animations/undock/
SAMSON and all SAMSON Extensions are free for non-commercial use. To get SAMSON, visit https://www.samson-connect.net.