Creating meaningful molecular animations is often a pain point for modelers who want to illustrate molecular docking events or transitions between bound and unbound states. Animations can clarify biomolecular mechanisms in communication with collaborators, for publications, or for presentations. But accurately portraying molecules approaching each other in 3D—and doing so smoothly—can become technically challenging and time-consuming.
Fortunately, SAMSON offers a convenient feature designed exactly for this purpose: the Dock animation. This animation lets you dynamically move groups of atoms or meshes from an automatically-selected starting configuration to their current position, which is treated as the docked state. The effect is a clear, visual trajectory that enhances understanding of molecular interactions—without the manual labor of positioning atoms frame by frame.
What is the Dock Animation?
At its core, the Dock animation in SAMSON is a motion effect applied between two keyframes. It moves atoms or meshes from a computed location to their “docked” state. The keyframes define the timeline. The animation’s amplitude (distance of movement) is determined automatically based on geometry, though it can be customized.
This can be particularly helpful for visualizing docking scenarios such as ligand-receptor binding, macromolecular association, or even the assembly of nano-objects.
How to Use It
- Select at least two structural nodes (e.g., molecules, residues) or meshes in the document. The first selection will act as the static target or receptor; the others will move toward it.
- If you want multiple nodes to be receptors, place them in a folder and select the folder as the first item.
- If you don’t select anything, SAMSON will attempt to infer relevant nodes for the animation.
- Open the Animator panel (Ctrl+7 on Windows/Linux or Cmd+7 on macOS).
- Double-click on the Dock animation in the Animation panel. SAMSON generates the animation between two keyframes automatically.
- You can move these keyframes in the Animator timeline to adjust when the docking happens.
Customizing the Motion
The Dock animation isn’t just plug-and-play—it’s also customizable:
- Amplitude: To modify how far the atoms move before docking, use the Inspector.
- Timing: Adjust the timeline by shifting keyframes in the Animator.
- Smoothness: Fine-tune the interpolation using an Easing curve for more natural motion.
Visual Example
The following visual demonstrates the Dock animation in action, showing a molecular group transitioning smoothly into a binding position:
Real-World Applications
Several public projects on SAMSON Connect showcase the Dock animation in context. These include docking simulations like:
If you’re preparing a video abstract, presentation, or just want to visualize docking mechanisms in your system, the Dock animation can save time while producing results that are easy to understand and share.
To learn more about the Dock animation, visit the official documentation page: 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