Visualizing molecular docking is an essential part of many presentations in molecular modeling. Whether you’re showing how a ligand fits into a protein binding site, or preparing a video to share with collaborators or students, the process of creating smooth, accurate animations can be time-consuming or require advanced skills in traditional modeling tools.
The Dock animation feature in SAMSON simplifies that process, making it fast and intuitive to animate molecules as they move from a distant position to a docked one. This is especially helpful for structural biology, molecular dynamics, or drug design projects where you want to effectively communicate molecular interactions.
What is the Dock animation?
The Dock animation in SAMSON takes a group of selected atoms or meshes and animates them as they move toward their final, docked positions. These final positions are where the atoms are located when you apply the animation. SAMSON automatically generates starting positions away from these locations, giving you a ready-to-go animation of molecular docking dynamics.
Why it matters 🚀
If you’re working in molecular modeling, you likely need to show how molecules interact or bind. But setting this up manually—positioning molecules, scripting motions, ensuring they follow realistic paths—can be tedious. The Dock animation takes care of that with just a few clicks.
This feature is particularly useful when you want to:
- Explain binding mechanisms during a presentation
- Create instructional content for students or collaborators
- Prepare compelling visuals for grant proposals or publications
- Generate portfolio pieces if you’re demonstrating modeling work
How to use it
Here’s how you can apply a Dock animation in SAMSON:
- Select at least two structural nodes – The first will be treated as the static receptor, while the others will animate toward it. If you’re using multiple receptors, you can group them into a folder and select the folder first.
- Open the Animation panel in the Animator interface.
- Double-click the Dock effect from the list of animation effects.
- That’s it – SAMSON will create two keyframes and animate the selected molecules moving to their target positions.
You can adjust the animation by editing the timeline keyframes or modifying properties like the amplitude of motion with the Inspector. For more control, experiment with the easing curve to change how the speed varies with time.
Tip: Animate Without Hassle
If you don’t make a selection before applying the Dock animation, SAMSON will make an educated guess about which atoms to move. While this helps streamline simple animations, making careful selections will give you clearer control over the outcome—particularly in complex systems.
See it in action
This example shows how a ligand docks into its receptor. You can reposition the keyframes on the animation timeline to speed up or slow down the docking process, giving you flexibility over the pacing of your final presentation.
To explore more about the Dock effect and see example projects, check the full documentation page: Dock animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at www.samson-connect.net.