In molecular modeling, visual clarity matters—especially when you’re dealing with complexes where molecules interact closely, such as in docking studies or protein-ligand interactions. If you ever presented your model and found yourself thinking, “I wish I could just show how these components separate naturally,” then you’re not alone.
Whether you’re preparing an animation for a presentation or just exploring the assembly of molecular structures, the Undock animation in SAMSON offers a quick and intuitive way to visualize molecular components separating from a docking state. It’s both helpful and easy to use—once you know how.
Why undocking helps in molecular model visualization
When visualizing complex molecular systems, clarity can make a big difference. Undocking animations allow you to:
- Show separation of ligands from receptors in a way that mimics plausible trajectories.
- Make molecular animations educational and more comprehensible to non-expert audiences.
- Prepare cleaner visuals for movies, posters, or interactive documents.
How the Undock animation works
The Undock animation detaches selected groups of atoms or entire meshes from their presumed docked positions. What makes it effective is that the final positions are automatically computed—there’s no need to manually set trajectories. Instead, the system determines a direction and amplitude to separate the components in a presentation-friendly way.
Setting up the animation in SAMSON
Here’s a brief walkthrough on applying the Undock animation:
- Select nodes or meshes: Choose at least two structural elements. The first selected node acts as the static receptor. If you want multiple items to act as one receptor, you can group them in a folder and then select the folder.
- Apply the Undock effect: Open the Animation panel in the Animator, and double-click “Undock.” The animation will be applied between two keyframes. You can move and edit the keyframes to suit the timing of your presentation.
Controlling the animation
The movement’s amplitude is calculated automatically when you first apply the animation. However, if you want to fine-tune it—for example, to make it more subtle or more pronounced—you can use the Inspector to adjust the amplitude. Additionally, you can customize how smoothly the movement evolves over time by modifying the easing curve.
Better communication through better presentation
This feature is especially helpful when training students, building tutorials, or communicating with collaborators who are visual learners. Animations such as Undock bring attention to spatial relationships and transitions, two things that static images often fail to communicate effectively.
Additionally, you’re not limited to undocking. Combine it with other animations like Dock, Move Atoms, or Hold Atoms to produce more expressive molecular narratives.
Learn more in the full documentation here: https://documentation.samson-connect.net/users/latest/animations/undock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.