When preparing molecular presentations or exploring molecular complexes, molecular modelers often face the challenge of clearly visualizing how different molecular groups interact — or separate. Whether it’s for highlighting binding interactions, presenting docking results, or explaining receptor-ligand dynamics, it helps to be able to animate how parts of a molecular system dissociate.
This is where the Undock animation in SAMSON can make a difference. With minimal input, the Undock effect allows you to animate the separation of selected nodes or meshes in a scene, making your presentations both informative and easier to understand.
What Is the Undock Animation?
The Undock animation undocks molecular groups or meshes from a reference position — typically representing a docked or bound state — and moves them away automatically based on their initial position. This motion is particularly useful for illustrating unbinding events or preparing educational visuals that showcase molecular dissociation.
When Would You Use It?
- To demonstrate how a ligand leaves a binding pocket
- To visualize the change in structure before and after molecular docking
- To enhance understanding in educational settings
- To present transition states or structural rearrangements in dynamic presentations
How to Add the Undock Animation
Here is a step-by-step guide to use the Undock animation:
- Select at least two nodes (e.g., molecules or meshes) in your document. The first selection will be considered the receptor (static), and the remaining nodes will undock from it.
- If your receptor is composed of multiple nodes, group them into a folder and select the folder first.
- Open the Animator ( Ctrl + 7 on Windows / Cmd + 7 on Mac).
- In the Animation panel, double-click on the Undock animation.
- Between two keyframes, SAMSON will compute and animate the separation for you automatically.
Adjusting the Animation
Once the animation is inserted, you can:
- Move keyframes to control when the undocking starts and finishes.
- Adjust the amplitude of undocking via the Inspector.
- Tweak easing curves if you want a non-linear motion progression (e.g., to simulate acceleration or deceleration between frames).
Example Use Cases
Want to see actual examples? Check the documents on SAMSON Connect that use the Dock animation — the inverse function — to visualize molecular associations:
You can easily adapt these to apply the Undock animation instead and study or present the reverse process — such as ligand unbinding or complex dissociation.
Final Thoughts
Clear communication of structural changes in molecular systems can be critical, whether you’re publishing a paper, teaching students, or sharing results with colleagues. The Undock animation helps bridge the gap between static models and dynamic understanding.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.