Visualizing molecular interactions is key to understanding complex biological processes, especially when communicating with collaborators or during presentations. Molecular modelers often need to show how a ligand undocks from a receptor to highlight binding interactions, conformational changes, or docking reversibility. This can be challenging to animate without manual editing or external video production tools.
The Undock animation in SAMSON provides a simple, integrated way to generate undocking animations, helping modelers and researchers visually communicate molecular mechanisms with minimal effort.
What is the Undock animation?
The Undock animation in SAMSON smoothly separates a selected group of atoms or meshes from their initial (“docked”) position to an automatically computed final position away from the receptor. It’s a dynamic way to show how molecular complexes disengage over time—useful for illustrating docking simulations, exit pathways, or simply creating eye-catching visuals for talks and videos.
The final positions are automatically computed to move away from the docking site, ensuring clarity without requiring user-defined trajectories.
When is it useful?
This animation is particularly helpful for:
- Highlighting the unbinding of a ligand from a protein in educational or research presentations
- Showing the reverse motion in a docking simulation
- Demonstrating simple exit paths of small molecules
- Creating intuitive, automated visuals for pathway design or animation reels
How to use it
To apply the Undock animation in SAMSON:
- Select at least two structural nodes or meshes—the first will act as the receptor, and the others (e.g., ligands) will be animated. You can also group multiple receptor nodes into a single folder and use that as the static selection.
- Open the Animator (> Animation panel) and double-click on the Undock animation effect.
- Adjust the keyframes as needed—move them along the timeline to control animation speed and position.
- To refine the animation, open the Inspector to tweak the amplitude or apply easing curves for smoother transitions.
It’s worth noting that if you don’t explicitly select objects, SAMSON will attempt to automatically detect what should be undocked. However, for precision and control, it’s better to define selections manually.
Customizing your animation
Once the animation is added, SAMSON calculates movement amplitude automatically. If the displacement is too small or too large, or you’d like to match it to another animation sequence (e.g., a docking-reverse), you can:
- Inspect and adjust the amplitude via the Inspector
- Change the easing curve to control how the movement accelerates or decelerates across frames
These adjustments allow you to craft animations that are stylistically consistent with the rest of your project or presentation material.
Consider combining with other effects
You can pair Undock with animations like Dock, Hold atoms, or Move atoms to choreograph larger animation sequences that tell a full molecular story—from approach, to binding, to release.
To learn more and explore sample presentations that use docking/undocking animations, visit the full Undock animation documentation: https://documentation.samson-connect.net/users/latest/animations/undock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get started today by downloading SAMSON at https://www.samson-connect.net.