In molecular modeling, showing how ligands bind to receptors is key when presenting your research. But visualizing this interaction clearly and smoothly can quickly become time-consuming. If you’ve ever struggled with showing how a molecule docks into a protein pocket in a way that makes sense to colleagues or reviewers, you’re not alone.
The Dock animation in SAMSON offers a streamlined way to animate the binding of molecules to their targets—think of it as a presentation tool that adds clarity without requiring hours of manual adjustment. This post walks you through how to create this animation and why it can make your molecular presentations more effective.
What the Dock Animation Does
The Dock animation creates a transition between two states of a molecular structure: a starting point (in which selected atoms or meshes are away from their final position), and a final point that corresponds to the target docking configuration. The animation smoothly moves the selected elements to their docked locations.
This can be particularly useful in presentations, educational content, or when preparing a figure for a paper to illustrate binding interactions dynamically. Unlike static images, animations are more intuitive for showing how components interact over time or between states.
How to Set It Up
To apply a Dock animation:
- Select at least two nodes (atoms, groups, or meshes). The first one acts as the receptor and stays static. The others will move toward it.
- If you’d like more than one static node (e.g., several chains forming a receptor), group them in a folder and select this folder first.
- In the Animation panel of the Animator, double-click on the Dock animation.
The software automatically computes starting positions for the moving nodes, pulling them back from the docking point to create a visible motion path.
Customizing the Motion
By default, the Dock animation spans the current keyframes in your animation timeline. But you can customize how the movement looks:
- Keyframe Adjustment: Move keyframes in the Animator timeline to control the speed and timing of the docking.
- Amplitude: The distance traveled is set automatically at creation. To adjust it, use the Inspector panel.
- Easing Curve: Smoothen or alter the animation’s fluidity with the easing curve options.
Example Use Cases
Wondering what the final result might look like? Check out these examples directly on SAMSON Connect:
Why It Matters
Molecular modelers often need to represent complex dynamics and interactions in ways that are accessible to others—from students to collaborators. The Dock animation bridges that communication gap. It doesn’t simulate the docking process (e.g., energy minimization) but provides a clear, clean way to show molecular movement in context.
To learn more about how to use the Dock animation, visit the full documentation 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 at https://www.samson-connect.net.