If you’ve ever prepared a molecular presentation and wanted to clearly show a ligand docking into a receptor, you may have run into a common challenge: animating the motion in an intuitive, visually appealing way—without spending hours tweaking coordinates or scripting complex transformations.
This is where SAMSON’s Dock animation comes in. It’s designed for this exact pain point: enabling quick, automatic docking animations that are visual and reproducible, perfect for communicating your molecular model in research papers, presentations, or teaching materials.
What is the Dock Animation?
The Dock animation in SAMSON makes selected atoms or meshes animate toward a fixed reference—typically a receptor structure—reaching what is presumed to be their docked state. The beauty of the Dock animation lies in its simplicity: it automatically calculates starting positions for the mobile groups, away from the final, docked configuration. That means you don’t need to set up docking poses manually.
The result? A seamless molecular movement that captures the idea of selection-specific docking, whether you’re showcasing ligands finding their binding sites or large domains snapping into place.
How to Use It
Here’s the general workflow:
- Select nodes or meshes: Choose at least two structures in your document. The first selected node is treated as the static receptor; all subsequent selections will move relative to it.
- Optionally group receptors: Want multiple receptor elements? Put them in a folder and select the folder first.
- Apply the Dock animation: Simply double-click the Dock effect in the Animation panel inside SAMSON’s Animator.
- Adjust keyframes: The motion occurs between two keyframes. Move the animation handles to adjust the timing.
Customization and Control
By default, SAMSON automatically computes the movement amplitude. If you want fine control, use the Inspector panel to adjust parameters such as the starting distance. You can also modify the easing curve to change the speed profile of the motion over time.
Why This Matters
Animations are often viewed as aesthetic overlays, but in molecular visualization they serve an educational purpose. Showing the process of docking, even in schematic form, helps communicate binding mechanisms, relative orientations, and the role of molecular flexibility. Instead of freezing the scene in a single pose, the Dock animation allows movement to be part of the story.
Whether you’re teaching protein-ligand interaction in a classroom or illustrating your latest structure-function data, it’s an effective visual cue that requires minimal setup. And since it’s baked right into the Animator panel, you don’t need to install anything extra.
See It in Action
Here’s a real example of the Dock animation at work:
You can also find publicly available projects on SAMSON Connect that use this feature—like the 2AZ8 and 5SAT molecular systems.
Learn more about the Dock animation in the documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.