In molecular modeling, visual storytelling plays a surprisingly important role. Whether you’re preparing a scientific talk, teaching structural biology, or simply trying to understand how two molecules interact—or stop interacting—animation can provide clarity that static images often can’t. One common scenario: showing how a ligand or any structural group dissociates from its binding site.
Meet the Undock animation in SAMSON.
The Undock animation lets you illustrate a group of atoms or a mesh moving away from a position where it is considered docked—say, a ligand from a receptor, or a protein subunit detaching from a complex. Instead of manually defining movement, SAMSON automatically computes the direction and distance of the motion, making it easier and faster to generate meaningful visuals.
Why It Matters: A Common Modeling Pain
Researchers often want to depict dissociation events or show hypothetical states in presentations. Manually animating such events can be time-consuming, especially when you’re working with multiple nodes or when you don’t want to tweak dozens of atom positions by hand.
The Undock animation removes that friction. It’s intelligent enough to compute where the atoms should move, and it’s easy enough to use without requiring scripting or advanced animation knowledge.
How It Works
To apply the Undock animation in SAMSON:
- Select at least two structural nodes or meshes in the document. The first selected node is treated as the static receptor; other nodes are animated away.
- If you want multiple structures to act as the receptor, place them in a folder, then select that folder as your first node.
- If no selection is made, SAMSON attempts to guess the relevant nodes.
- Double-click on the Undock option in the Animation panel within the Animator.
You’ll see the undocking animation between two keyframes by default. You can adjust the amplitude of the movement through the Inspector, and change the interpolation using the Easing curve.
Tips for Better Animations
- Use folders strategically to group receptor elements—this helps keep your presentations tidy and descriptive.
- Try combining Undock with other animations like Dock or Hold Atoms to show reversible processes or compare scenarios.
- Adjust the keyframes to fine-tune timing and synchronize the undocking event with other ongoing animations.
See It in Action
Here’s an example of the Undock animation in SAMSON:
While the animation clip above uses the old Animation menu, the current way to access Undock is via the Animation panel in the Animator.
Want to Explore More?
SAMSON also offers animations like Dock, Move Atoms, and Hold Atoms, which can be creatively combined for richer molecular storytelling.
To dive into the full details and additional examples, head to the documentation page: 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.