Communicating molecular mechanisms clearly is a recurring challenge for molecular modelers, especially when presenting ligand-receptor interactions, docking pathways, or structural transitions. One simple but often overlooked pain point is illustrating how a ligand undocks from its receptor. This step is not only essential to represent in animations and presentations, but also a powerful way to validate molecular conformations or support hypotheses visually.
SAMSON provides a user-friendly solution to this with its Undock animation. If you’ve ever struggled with animating an exit trajectory after docking in a molecular visualization tool, this feature may save you significant time — and frustration!
What does “Undock” actually do?
The Undock animation moves groups of atoms (or entire meshes) away from their originally docked configurations. The final undocked positions are automatically computed based on the geometry of the scene, ensuring a clean separation for visual purposes. This animation works well in both realistic molecular scenarios and abstract visual storytelling.
Getting Started — Applying the Undock Animation
To set up an Undock animation in SAMSON:
- Select at least two structural nodes (i.e., atoms, molecules, or meshes). The first one will be the static receptor. All others will animate away from it.
- If you want multiple nodes to remain static, you can place them in a folder and select the folder as the receptor.
- Then open the Animation Panel in the Animator and double-click the Undock animation effect.
Tip: If nothing is selected, SAMSON will do its best to infer what to undock — but it’s safer to make selections explicitly, especially when presentation quality matters.
Tuning the Animation
The Undock animation creates a temporal transition between two keyframes. You can:
- Manually adjust keyframes to change timing.
- Change amplitude of the movement using the Inspector.
- Refine motion smoothness with Easing Curves to get linear, ease-in/ease-out, or other interpolation styles.
These small adjustments can create a major difference in clarity when explaining molecular events.
A Simple Yet Effective Example
Here’s a short excerpt from a presentation showing the Undock animation in action:
Animations like this make a huge impact when added to a presentation or a grant proposal. They clearly convey movement and spatial relationships that static figures often cannot.
Good to Know
- The amplitude is computed automatically when the animation is created, so you don’t need to guess displacement values.
- The Undock effect works well when paired with other animations like Dock or Move Atoms.
- If you previously saw the Animation menu in tutorials or videos, note that animations are now accessed via the Animation Panel in the Animator interface.
Why This Helps
Using SAMSON’s Undock animation bridges the gap between raw simulation data and engaging, informative visual communication. Whether you are preparing for a workshop, teaching, or writing a paper, showing conformational pathways with clear, smooth animations improves understanding and accessibility of your work.
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 get SAMSON at https://www.samson-connect.net.