One of the challenges molecular modelers frequently face is how to visually simulate the departure of a ligand or component from a molecular complex. Whether you’re preparing a presentation, investigating structural hypotheses, or producing educational material, animating this process in a controlled and interpretable way is not always straightforward.
This is where SAMSON’s Undock animation becomes especially useful. It allows you to undock one or more groups of atoms or meshes from a reference receptor group, with final positions automatically calculated to show a clear separation. This is particularly handy to simulate molecular departure events, channel openings, or initial stages of molecular rearrangements—without the need for manual transformation algorithms or scripting.
Setting up the Undock Animation
Start by selecting two or more structural nodes or meshes in your SAMSON document. The first node in your selection will act as the static receptor, and the others will be the moving components. If you have multiple receptor nodes, simply place them in a folder and select the folder first. If nothing is selected, SAMSON will attempt to infer the setup—but for precision, manual selection is recommended.
After making your selection, open the Animator panel (you can use Ctrl + 7 or Cmd + 7), then double-click on the “Undock” animation effect to insert it between two keyframes. This creates a smooth animated motion where selected moving nodes undock away from the initial structure.
Adjusting Movement and Easing
The amplitude of the motion is computed automatically during creation, but for fine-tuning, you can inspect the animation via the Inspector panel. Here, you’ll be able to increase or decrease how far the structures move. You can also tailor the flow of animation using easing curves, giving a more natural or deliberate motion profile to the undocking behavior.
For example, a slow easing-out curve may be ideal for teaching videos, while a constant motion curve fits demonstration purposes better. Moving keyframes on the animation timeline also allows you to regulate speed and timing effectively.
A Note on the Interface
Earlier versions of SAMSON used an “Animation” menu, but this menu is no longer available. All animation tools are now accessible through the Animator panel. The functionality remains the same, but with improved consistency and easier access to tools.
Why Use Undock?
The Undock animation bridges intuitive design with technical necessity. It allows molecular modelers to:
- Simulate ligand exit paths.
- Visually separate bound components for illustration.
- Create smooth disengagement animations without manual modeling.
It’s a time-saver especially when preparing scenes for presentations, video generation, or collaborative demonstrations. No coding required—just click, select, and tweak.
Example Snapshot
In the example above, the Undock animation automatically moves a ligand away from its receptor, providing an immediate, intuitive visualization of structural separation.
To learn more, visit the full documentation here: Undock Animation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.