Molecular docking is a fundamental part of computational chemistry and drug design workflows. But when you want to visualize docking events—whether for a presentation, teaching, or analysis—it can feel surprisingly tedious to make atoms move smoothly and meaningfully in 3D space. That’s where the Dock animation in SAMSON comes in.
This post explains how to leverage the Dock animation to create clear and informative visualizations of docking motions, from setting up the animation to controlling movement precision. This technique is particularly useful for researchers preparing visual materials for publications, teaching or communicating molecular mechanisms to broader audiences.
Why use the Dock animation?
It’s often challenging to depict the process of molecules finding their binding spots. Static before/after images leave out the story. The Dock animation lets you automatically generate the full motion—from unbound to bound state—directly in your molecular scene.
It saves time too. No need to animate individual atoms manually or calculate paths. With a few clicks, you can generate smooth animations where ligands or molecular fragments move toward their binding poses convincingly.
Setting it up
Here’s how to configure a Dock animation in SAMSON:
- Select two or more nodes (atoms or meshes) in the document. The first selection is treated as the stationary receptor. All others are mobile ligands.
- If you want a group of nodes to act as receptor, create a folder, place those nodes inside, and select the folder first.
- Open the Animator and double-click on the Dock animation in the Animation panel.
Once activated, the animation automatically computes starting positions away from the docked state to simulate an approach motion.
Customizing the animation
By default, the motion’s amplitude is computed automatically based on spatial separation. But you can fine-tune this:
- Open the Inspector panel to change the amplitude.
- Tweak the easing curve to control how smoothly the transition unfolds across time.
It’s also possible to reposition the animation keyframes manually on the timeline to synchronize the docking movement with other presentation elements.
Tips for better visuals
- Use the Dock animation in combination with other animations like Undock or Hold Atoms to depict mechanisms or simulate reversibility.
- Highlight paths between start and end positions by showing trails or ghost conformations.
- If the receptor is complex (e.g., a full protein), using a folder makes management cleaner and avoids unintended movements.
Example in action
Below is an example animation of a ligand docking into a receptor. This can be generated in less than a minute using the techniques above:
If you’re teaching or presenting molecular mechanisms, this kind of animation can help audiences grasp spatial relationships and dynamic behavior more intuitively than static visuals.
Conclusion
The Dock animation effect provides a straightforward yet flexible way to communicate molecular docking visually. Whether you’re teaching, publishing, or simply trying to understand a structure better yourself, this feature adds clarity without requiring animation expertise.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.