Designing compelling molecular animations often becomes a bottleneck in structural biology and molecular modeling—especially when trying to clearly present docking events or compare bound and unbound states. In many cases, modelers want to show how ligands or components fit with a receptor, but manually configuring smooth and synchronized movements can be tedious and prone to error.
The Dock animation in SAMSON provides a simple and automated way to present docking processes visually. Whether you are preparing educational material, papers, or presentations, you can effortlessly animate molecules transitioning into their docked state using predefined keyframes. Here’s how it helps and how to use it effectively.
What does the Dock animation do?
The Dock animation takes the current structure of selected atoms, groups, or meshes as their final “docked” state. When triggered, it automatically computes a reasonable starting position for each component, typically away from the target site, and animates its motion toward it between two keyframes. The result: a dynamic and smooth docking motion that communicates structure-function relationships effectively.
How to apply it
The process is straightforward:
- Select at least two nodes or meshes. The first node becomes the static receptor. If you have multiple receptor components (e.g., pockets), group them in a folder and select the folder first.
- Apply the animation: double-click “Dock” in the Animation panel.
- Adjust keyframes: move the animation keyframes as needed to fit your scene timing. The receptor stays in place while the selected components move from a starting point into the binding site.
One smart aspect is that if you don’t select nodes manually, SAMSON will try to infer them based on spatial relations—helpful during exploratory modeling workflows.
Refining your animation
While the default animation is automatically generated, you can fine-tune its behavior. For example:
- Amplitude of motion: open the Inspector to modify how far initial positions are from the docking spot.
- Smoothing the motion: use Easing curves to control acceleration and deceleration of the animation. This gives your presentation a more realistic or pedagogically useful pace.
Use case: Comparative docking setups
Suppose you’re demonstrating how different ligands fit into the same binding site. Instead of building new poses from scratch or overlaying static snapshots, you can create multiple Dock animations within the same scene. With carefully chosen timings, you can “cycle” through different docking events visually, and even export them as movies for your figures or presentations.
Need a head start? Check out these SAMSON Connect examples that already use Dock animations:
To learn more about the Dock animation and how it fits within SAMSON’s animation toolkit, visit the full documentation: Dock Animation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.