A frequent challenge in molecular modeling is clearly conveying how molecules interact—especially when it comes to docking. Static images can’t capture the nuances of molecular movement, and scripting animations manually can be time-consuming and unintuitive. If you’ve ever wanted a fast yet flexible way to show a molecule docking to a receptor, good news: the Dock animation in SAMSON does exactly that, and it’s easier than you might think.
What is the Dock Animation?
The Dock animation moves groups of atoms or meshes from automatically computed starting positions to their final, receptor-bound configurations. Rather than manually defining a docking transition, SAMSON calculates a starting point for the animation that ensures a clean and visually meaningful approach toward the binding target. The result? An intuitive, dynamic visualization of molecular binding events.
This can be particularly useful when preparing presentations, exploring binding pathways, or simply adding clarity when communicating your molecular modeling work with colleagues or collaborators.
Getting Started: Setting Up a Dock Animation
Here’s a practical, step-by-step summary to get you started with the Dock animation:
- Select your system: In your document, select at least two structural nodes or meshes. The first one will serve as the static receptor; the others will be animated.
- Group receptors if needed: If your receptor is composed of multiple nodes, you can place them in a folder and select the folder as the receptor.
- Add the animation: Double-click the Dock effect in the Animation panel of the Animator.
- Adjust timing: Move the animation’s keyframes as needed to fit your presentation or analysis timeline.
- Tweak properties: Use the Inspector to adjust the amplitude (strength) of the movement or interpolate motion between frames with different easing curves.
When and Why to Use Dock Animations
Animations like this are particularly valuable in visual communication. Whether you’re demonstrating molecular dynamics in a conference talk or teaching students how ligands enter a binding pocket, a Dock animation can replace dozens of static images or abstract descriptions.
It’s also a useful tool for internal iterative modeling. When you’re comparing multiple docking hypotheses or highlighting small differences in movement or positioning, using animation can help you spot patterns or inconsistencies that would otherwise go unnoticed.
Visual Example
Below is an example GIF that shows the Dock animation in action:
Try Real Examples
If you’d like to explore how Dock animations are used in real cases, you can open the following presentations available on SAMSON Connect:
These examples can serve as templates to get you started or inspiration to explore other animation effects like Undock, Hold atoms, or Move atoms.
To learn more, visit the full documentation for the Dock animation: https://documentation.samson-connect.net/users/latest/animations/dock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.