If you’ve ever spent too long trying to create a smooth molecular docking animation—manually adjusting atomic positions or writing complex scripts—you’re not alone. Visualizing docking movements between molecules or between a ligand and a receptor can be time-consuming, especially when the goal is to communicate mechanisms in research articles, presentations, or educational videos.
Fortunately, SAMSON offers a built-in Dock animation that drastically simplifies this process, helping you animate docking interactions between atoms or 3D meshes directly within its visual interface. In this blog post, we’ll show you how to take advantage of the Dock animation in SAMSON using the Animator panel and keyframes, without needing advanced animation skills.
What is the Dock Animation?
The Dock animation moves selected groups of atoms or 3D objects from automatically computed starting positions back to their target—or “docked”—positions. This is very useful for simulating how ligands bind to receptors, visualizing parts assembling into a larger structure, or even demonstrating how flexible regions return to a preferred conformation.
Getting Started: Your First Dock Animation
Here’s how to set up a Dock animation in SAMSON:
- Select your components: Choose at least two structural nodes or meshes in your document. The first one acts as a static reference (like a receptor), and the rest are animated. If multiple receptors are needed, group them into a folder and select that folder first.
- Activate the Dock effect: In the Animator’s Animation panel, double-click on the Dock animation effect.
SAMSON then automatically computes initial positions for the animated nodes, from which they will move to their docked positions between two keyframes. The cool thing? This means you don’t need to manually define both starting and ending locations—just the final configuration matters.
Using Keyframes to Control Timing
Once the Dock animation is applied, you’ll see two keyframes in the Animator timeline. You can reposition these to control when the docking motion occurs during your animation sequence. Need the docking to happen earlier or last longer? Just drag the keyframes accordingly.
Fine-Tuning the Animation
You can inspect the Dock animation in the Inspector to tweak the amplitude of movement. This lets you exaggerate or minimize the entry movement path based on your communication needs.
Also, if you want to change how smoothly the atoms move, you can modify the Easing curve. This affects the acceleration of motion, and can help you match the feel of real-world dynamics or add dramatic effect to your animation.
Example Docking Visualizations
Want to see Dock in action? Check out the following documents that include this animation:
This feature can really save you time while enhancing how clearly you present molecular interactions—whether in teaching, communication with collaborators, or sharing your work on social media or in presentations.
To explore more, visit the full documentation page on Dock animations here: https://documentation.samson-connect.net/users/latest/animations/dock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.