One challenge molecular modelers frequently face is how to effectively showcase binding poses and docking sequences in a clear, visual way — both for presentations and team communication. Whether you’re demonstrating a ligand binding to a receptor, pieces of a supramolecular assembly forming, or simply want to animate molecular alignment, the Dock animation in SAMSON offers a flexible and intuitive solution.
Rather than laboriously arranging keyframes by trial and error, the Dock animation automatically positions atoms or meshes to “dock” into a target location you specify. This minimization of manual steps helps users focus on the science of the interaction — not the animation workflow.
What Does the Dock Animation Do?
It animates one or more atoms or meshes so that they move from automatically determined starting positions toward a receptor or docking site — which can be an individual node or a group of nodes. These movement paths are calculated at the moment the animation is created. The position to which the atoms move represents the conformation or final bound structure you originally chose.
The movement occurs over a timeline controlled via keyframes in the Animator panel. You can move these keyframes around to speed up or slow down the docking.
Why Use It?
- Visually demonstrate how components move into final positions during molecular docking scenarios.
- Create understandable animations for papers, grant applications, or educational content.
- Avoid complex manual movement setups — final positions are used as inputs, and initial positions are automatically generated.
- Works on both atoms and meshes, suitable for hybrid simulations or coarse-grain models.
How to Apply the Dock Animation
Here’s how to apply the Dock animation step-by-step:
- Select your nodes or meshes: Choose at least two nodes in your document. The first will be the receptor (static), and the others will move toward it. To use multiple nodes as the receptor, group them into a folder and select that folder first.
- Open the Animator panel: Navigate to the Animation panel in SAMSON.
- Double-click Dock: This adds the Dock animation to the timeline.
- Adjust keyframes and amplitude: Drag the keyframes to control animation timing. To change how far nodes move before docking, right-click on the Dock animation in the timeline and inspect it.
- Customize easing: You can fine-tune the feel of the animation by modifying the easing curve, accessible from the Animator panel.
Example in Action
The example below demonstrates how a group of atoms smoothly transitions into a docking configuration using the Dock animation effect:
Tips
- If nothing is selected when you insert the animation, SAMSON will try to guess the target and moved components automatically.
- You can combine Dock with other animations like Undock or Move atoms for interactive sequences.
Learn more about the Dock animation in SAMSON documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.