In molecular modeling, it’s often necessary to communicate how molecules interact, bind, or dissociate from each other. One common yet often cumbersome task is illustrating how a ligand undocks from a receptor in a clear, dynamic way. Explaining docking poses through static images or descriptions can fall short in presentations or publications. If you’ve ever spent an hour manually crafting frames to achieve this, only to end up with a clunky animation, SAMSON’s Undock animation effect may save you a lot of time—and frustration.
Designed for molecular presentations, the Undock animation in SAMSON lets you animate molecules or object groups as they move away from what are assumed to be their docked positions. SAMSON computes the direction and movement amplitude automatically, making this a fast and reproducible method for showing binding site exits, drug-receptor dissociation, or merely emphasizing conformational flexibility.
When and why should you use the Undock animation?
If you’re presenting a ligand-protein interaction, showing how ligands dissociate can highlight directionality, potential exit pathways, or simply underscore molecular motion in your system. The animation enhances clarity for viewers—especially those unfamiliar with the exact binding mechanisms. It’s not only useful for teaching but also for research communication and molecular design discussions.
How to implement it in your scene
Applying the Undock animation takes just a few steps:
- Select at least two nodes or meshes: The first one acts as the static receptor, and the rest are assumed to move.
- If you need multiple static elements (e.g., multiple parts of a receptor), group them in a folder and select that folder first.
- Double-click the Undock animation effect in the Animator’s Animation panel to apply it.
- Adjust keyframes in the Animator to control timing and movement.
The direction and amplitude of the undocking motion are automatically calculated when the animation is created, but for more control, you can use the Inspector to tweak the movement amplitude and the easing curve to adjust how smoothly the animation unfolds across keyframes.
Tips for better animations
- Use keyframes creatively: You can animate partial undocking over time or synchronize multiple molecules in one sequence.
- Combine with the Dock effect: For bidirectional interaction presentations (such as bind-then-unbind workflows), use Dock and Undock in sequence.
- Preview your work using the Animator: You can visually fine-tune the trajectory and pace to match your scientific message.
Troubleshooting: what if nothing is selected?
If you forget to select nodes before applying the Undock animation, don’t worry—SAMSON attempts to infer the relevant nodes based on the scene. Nonetheless, selecting nodes explicitly ensures more predictable results.
You can explore some example documents demonstrating related animation effects, such as the 2AZ8 Dock animation, available on SAMSON Connect.
Clear, simple animations can go a long way in improving scientific communication. By giving your audience a better understanding of molecular motions, you bridge the gap between static data and dynamic processes.
To learn more about how the Undock animation works, visit 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.