Creating compelling molecular presentations can be time-consuming—especially when you want to visually demonstrate how molecules interact. A common challenge for structural biologists and molecular modelers is to simulate docking mechanisms with clarity and realism, for publications, teaching, or presentations. Fortunately, the Dock animation in SAMSON provides a simple, visual solution that automatically generates a docking process between molecular fragments with minimal effort.
Why Dock Animations Matter
In molecular science, animations often clarify what static images cannot: how molecules come together. Whether you’re trying to depict protein-ligand docking or demonstrate supramolecular assembly, it can be tedious to position and interpolate structures manually. The Dock animation simplifies this step significantly. You define your final docking positions, and SAMSON computes the starting positions automatically—away from where you want them to dock. Then it animates a visually pleasing and realistic docking motion.
How It Works
The Dock animation works by anchoring one or more structures (the receptors) while animating others (ligands, subunits, etc.) from computed starting positions to the docking site. The only required step is to select at least two nodes or meshes within your SAMSON document:
- The first selected node will act as the receptor—it remains static.
- Other selected nodes will be animated toward the receptor.
This creates a quick, dynamic visualization of molecular docking between the two states (starting and final configurations). You can easily adjust the timing by interacting with the two generated keyframes, moving them further apart or closer together depending on the duration you want.
Make It Even Better
Once you’ve added the animation, you can fine-tune it with SAMSON’s Inspector. For example, you can:
- Change amplitude: Want your moving node to start closer or farther away from the receptor? You can customize the distance traveled by adjusting amplitude.
- Set an easing curve: This defines how the animation interpolates between frames (e.g., linear movement vs. easing in/out), giving your docking a more natural feel, especially useful for teaching or illustrative videos.
Tips to Get Started
- If you want multiple nodes to act as receptors, place them in a folder and select the folder first.
- If nothing is selected, SAMSON will guess what should be animated—but it’s best to be explicit to avoid confusion.
- Access the Dock animation from the Animation panel inside the Animator, not the old Animation menu.
See It in Action
Here’s a visual example showing how a molecule can be docked dynamically to a receptor using this animation effect:
In just a few clicks, you can generate animations like these and incorporate them into your presentations or exported movies. Want to see real-world cases? Check out these public examples built with the Dock animation:
This feature is a great way to level up your structural biology visuals—without needing to script or manually animate movements frame by frame.
To learn more, visit the full documentation page for Dock animation here.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.