Preparing a molecular animation that accurately conveys a binding mechanism or illustrates structural complementarity is often more work than expected. Whether you’re crafting a visual to accompany a publication or designing an animated explainer for your lab website, manually placing atoms and interpolating trajectories can be error-prone and time-consuming.
This is where the Dock animation in SAMSON can help. It offers a fast and intuitive way to animate groups of atoms or meshes moving into their docked positions, with minimal setup. If you already have a molecular complex and want to animate how parts of it come together, the Dock animation will enable this within seconds—and even computes the incoming path for you.
What does Dock do?
The Dock animation effect automatically calculates a smooth motion path that starts from a position away from the final docked configuration. In essence, it animates how one or more selected nodes (e.g., molecular fragments or meshes) “dock” onto a static receptor node or group of nodes.
The system intelligently generates initial positions away from the receptor, creating a natural-feeling approach. Between two keyframes, the mobile parts move into place, making it ideal for dynamic visualizations that show molecules assembling into a complete structure.
How to use it effectively
To apply the Dock animation:
- Select at least two nodes in your document—one will act as the static receptor (placed first in selection), and the others will animate toward it.
- If your receptor consists of multiple parts, group them into a folder and select that folder first.
- Then, open the Animation panel in the Animator and double-click on Dock. A Dock animation will be added between two keyframes.
Customizing the animation
SAMSON automatically computes the amplitude of the motion when the animation is created, but you can fine-tune it later:
- To change the amplitude, select the Dock animation in the Animator and use the Inspector.
- Want to make the movement more dramatic or subtle? You can adjust the Easing curve to control how the animation parameters (position, speed, etc.) interpolate over time.
Use cases
Here are a few situations where Dock animations can be especially helpful:
- Illustrating protein-ligand docking mechanisms without having to run a simulation first.
- Creating educational animations to show molecular assembly.
- Exploring how different parts of a macromolecular complex fit together.
Examples to explore
Want to see it in action? Check out these public SAMSON documents that use the Dock animation:
This kind of auto-generated animation is especially valuable when you need to quickly prototype visuals or communicate ideas, without launching a full molecular dynamics simulation.
To learn more, visit the full documentation page on Dock animation 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 and start building your own molecular animations here: https://www.samson-connect.net