Creating clear, informative presentations of molecular systems is one of the trickiest parts of structural modeling. Whether you’re explaining docking mechanisms in a classroom or preparing an impactful animation for a research publication, visual clarity is key. One common pain point modelers face is showing how molecules arrive at a binding site—without drowning viewers in unnecessary intermediate frames or complex motion paths. This is where the Dock animation in SAMSON offers a focused solution.
The Dock animation effect in SAMSON simplifies the animation of docking events by automatically moving molecular structures from an initial (auto-generated) position to their current one—which you define as the “docked” position. This is especially convenient for protein-ligand systems, assembling nanomaterials, or visually managing component-based simulations.
What does it do?
The Dock effect generates smooth movement between two keyframes, carrying selected atoms or meshes toward a fixed static receptor group. The first selected node (or folder, if you’re selecting multiple nodes) remains static, while the others animate toward it—mimicking docking behavior.
You don’t have to manually reposition atoms or set multiple intermediate frames. It’s a quick way to create a clean and understandable animation for presentations or videos that explain how molecules interact.
How to use it
- Step 1: Select at least two nodes (atoms, molecules, or meshes). The first one becomes the static receptor. To group multiple receptor components, place them in a folder and select the folder first.
- Step 2: Open the Animation panel in the Animator.
- Step 3: Double-click on Dock to apply the effect.
- Step 4: Adjust the keyframes if needed. You can move them on the animation timeline to change the start and end times of the docking movement.
Customization and control
Once applied, the Dock animation’s movement amplitude is computed automatically, ensuring that starting positions are reasonably distanced from their targets. If you want more control, you can:
- Inspect the animation and manually modify the amplitude in the Inspector.
- Customize how the animation speed varies over time by editing the easing curve.
Dock animations also work well in sequences involving other effects, like Undock or Move atoms, to simulate full interaction cycles or reveal mechanisms step-by-step.
Why it helps
Animations often involve a lot of trial and error. Getting the motion right so that it both conveys meaning and remains visually simple can take a lot of time. Dock removes that complexity by computing a clear motion from “far” to “docked” automatically. This is ideal for showing how ligands bind to macromolecular targets or assembling components in supramolecular systems.
For real-world examples, check out documents on SAMSON Connect that feature this animation:
To learn more, visit the full documentation page: Dock animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.