Anyone who’s built molecular presentations knows the challenge: how do you illustrate atoms or molecular groups smoothly docking into their target without manually keyframing every move?
This is where the Dock animation in SAMSON becomes particularly useful. It provides a straight-to-the-point, efficient way to create clean, visually effective docking animations without the hassle of scripting or hand-aligning conformations. Whether you’re building educational content, sharing molecular mechanisms, or demonstrating a docking result, this tool can help you create a clear story — and do it fast.
What the Dock animation actually does
The Dock animation moves selected molecules or meshes from automatically computed starting positions toward a user-defined final “docked” position. This gives the illusion of a docking process — for example, a small molecule binding to a receptor or a nanostructure snapping into a scaffold.
You don’t have to define both positions. Just select two or more nodes in your structure, and Dock will treat the first as the receptor (static), and the others as the moving parts. The starting positions are automatically calculated to be away from the targets, so your animation already contains spatial logic without manual tweaking.
Applying the Dock animation
Here’s how the process works:
- Select at least two nodes (atoms, molecules, or meshes).
- The first selected node is the receptor. Others will move and dock into place.
- To include multiple receptor components, group them in a folder and select the folder first.
- Open the Animation panel in the Animator, and double-click on Dock.
The animation is inserted between two keyframes. You can move those keyframes around in the timeline to control the animation duration. Once the animation is created, you can also adjust its amplitude (how far the moving nodes start from the target) and the easing curve (which governs how the motion is interpolated) through the Inspector.
When and why to use it
The Dock animation saves time and consistently produces effective visualizations, especially for:
- Presenting ligand docking in publications or lectures
- Demonstrating molecular assembly or binding in a mechanism
- Creating polished animations in seconds for student learning material
It can be hard to find a visualization tool that enables you to communicate complex spatial movements clearly without creating all the pieces manually. Dock provides a compromise between automation and control, eliminating tedious work but allowing adjustment when needed.
Visual example
Here’s a quick visual overview of the Dock animation in action:
Where to go next
- Try example documents that use Dock, such as 2AZ8 – Dock animation
- Explore related animations like Undock and Move atoms for more storytelling flexibility
To learn more, visit the full documentation page for Dock animation at https://documentation.samson-connect.net/users/latest/animations/dock/.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.