If you’ve ever prepared molecular animations for presentations, publications, or educational content, you know how time-consuming it can be to manually simulate atoms or molecular groups moving away from their binding sites. Whether you’re modeling a drug molecule departing from a protein pocket, or visualizing a ligand detaching from a catalytic site, the process isn’t always straightforward.
That’s where the Undock animation in SAMSON can save a lot of time and guesswork. It provides an efficient, reproducible way to move groups of atoms or meshes away from their docked configurations, producing smooth animations without manually adjusting paths.
Why Undocking Animations Matter
Molecular modelers often need to communicate binding and unbinding processes. When showing enzyme-inhibitor interactions, or teaching molecular recognition concepts, animations can bring abstract molecular events into focus. But traditional tools are either too rigid or too complex, and often require scripting or physics-based simulations to get plausible undocking behavior.
The Undock effect in SAMSON takes a different route: it gives you a quick way to undock atoms from a reference structure, automatically computing the displacement paths and keyframe transitions. It’s intended for informative and illustrative animations—not predictive molecular dynamics, but useful for highlighting structural features and spatial shifts.
How It Works
Here’s a typical workflow for using the Undock animation:
- Select the receptor and moving parts: Choose at least two structural nodes or meshes in the document. The first one acts as the receptor (static anchor).
- Apply the animation: In the Animation panel of the Animator, double-click the Undock effect to apply it between two keyframes.
- Adjust as needed: You can adjust the timing by moving the keyframes, or fine-tune the movement amplitude via the Inspector.
The amplitude is computed automatically based on spatial context, so the undocking creates a natural-looking separation. If multiple receptor parts are needed, you can place them into a folder and select the folder, making the process flexible.
Visual Example
In the example above, atoms move smoothly from docked to separated positions without needing to define detailed trajectories manually. This simplifies the process of illustrating what used to be complex to show.
Fine-Tuning the Effect
For greater control:
- Use the Inspector to adjust amplitude and other parameters
- Modify the Easing curve in the Animation panel to make motion smoother, faster, or more mechanical
These features are handy whether your goal is to make a short explanatory animation or an entire video showcasing a binding mechanism.
See It in Action
If you’re looking for presentations that already make use of SAMSON’s docking and undocking animations, check out public example documents on SAMSON Connect, such as:
You might find inspiration for your own animations there or even re-use materials for your next molecular illustration.
To learn more about the Undock animation, visit the official documentation page: 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.