If you’ve ever needed to visually represent how molecules come together during docking in your presentations or simulations, SAMSON’s Dock animation offers a smooth and intuitive way to make that happen. One common pain point for molecular modelers is the challenge of communicating binding processes clearly and effectively—especially when trying to represent static receptor-ligand interactions in dynamic, understandable sequences. This is where the Dock animation provides a practical solution.
What the Dock animation does is simple but effective: Starting from automatically calculated positions away from the receptor, groups of atoms or meshes are animated toward their final, docked positions. The docked positions correspond to the atoms’ or objects’ current places in your scene before applying the animation, which allows you to remain fully in control of both start and end states of molecular interaction.
Setting Up the Dock Animation
To apply the Dock animation, you first need to select at least two structural nodes or meshes in the document. The first node you select becomes the static receptor, while the remaining ones are treated as docking ligands or moving components. Want to use multiple nodes as the receptor? Group them into a folder and select the folder first.
Nothing selected? No problem—SAMSON will attempt to guess which nodes should be used as receptors and ligands. However, for reproducibility and clarity, manual selection is recommended.
Once your nodes are selected, open the Animation panel within the Animator workspace. Simply double-click the Dock effect to generate the animation. Your molecules will now smoothly transition between two keyframes. The default amplitude of the movement is determined automatically, but you can easily customize it.
Customization and Control
The animation is fully editable through SAMSON’s Inspector. You can change the amplitude—the distance between the starting and docked positions—delivering flexibility based on your presentation needs. Whether you’re illustrating minor conformational adjustments or large-scale molecular docking, you’ll have control over the range of motion.
You can also fine-tune the pacing of the animation between keyframes using the Easing curve. This adds even more realism to your docking simulations, letting you match the perceived speed and acceleration to the type of motion you are conveying.
When It’s Useful
This animation effect is particularly valuable in scenarios where you need to:
- Showcase ligand-receptor binding during a presentation or video demonstration.
- Help students understand molecular interactions with visually engaging transitions.
- Explain the docking process to collaborators or stakeholders with no deep scientific background.
Quick Example
This example shows how molecular components beautifully come together using the dock animation effect. This kind of visualization can make even a slide deck feel more like an interactive experience.
Learn more in the official documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.