Molecular modelers working with large structural datasets often face the challenge of visually demonstrating how different biomolecules interact. Whether you’re presenting receptor-ligand binding events, assembling complex biomolecular systems, or simply trying to communicate structural hypotheses, an animation can go a long way in helping others understand molecular dynamics.
The problem? Creating such animations is traditionally tedious and may require coding or handling external rendering tools — not ideal when you’re on a deadline or presenting to a broad audience.
This is where the Dock animation in SAMSON proves useful. It automates the visual docking process, animating multiple molecules or meshes as they move from computed start positions to a defined docked position — without writing any script.
How it works
The Dock animation requires that you select at least two structural elements — atoms or meshes. The first selected node acts as the receptor (remains static), and the others are moved to their docked positions. If your receptor is made of multiple pieces, group them into a folder and select the folder first.
To add the animation, simply navigate to the Animation panel within the Animator, double-click on “Dock,” and SAMSON handles the rest. The system automatically computes start positions and determines docking paths that are interpolated across the animation timeline using keyframes.
Adjustability without complexity
Once the Dock animation is applied, you can tune it easily:
- Move keyframes to change the duration or timing.
- Adjust amplitude in the Inspector panel in case the movement path feels too long or too short.
- Edit easing curves to control the interpolation between start and end positions using different timing functions (for example, accelerate then decelerate movements).
No scripting, no exporting, and no dependency on third-party software. Everything is handled directly within the Animator interface. This makes it ideal even for teaching or presentations, where the clarity and smoothness of the motion help simplify complex biomolecular behaviors.
Where can you use it?
The Dock animation is particularly well-suited for:
- Highlighting ligand binding and unbinding events.
- Demonstrating mechanical assembly or docking of protein subunits.
- Preparing animated slides without post-production tools.
Want to see it in action?
Try one of these published examples directly in SAMSON Connect:
To learn more about applying and customizing Dock animations in your projects, visit the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.