Whether you’re modeling a ligand leaving a receptor, simulating triggered molecular events, or simply creating more compelling scientific presentations, being able to animate molecular undocking is a powerful capability. But despite its potential, many molecular modelers struggle with the typical pain of visually representing motion in a way that is both accurate and easy to generate.
That’s where the Undock animation in SAMSON comes in. This built-in animation effect allows you to automatically simulate groups of atoms or meshes moving away from their docked (initial) positions. In this post, we’ll focus specifically on when and how to use the Undock animation effectively in your workflow, and how it can help you convey molecular processes more intuitively and professionally.
Why undocking matters
In molecular modeling, docking events are often a centerpiece of attention. But understanding what comes after—such as molecules leaving a binding pocket—can be just as important. Think of scenarios like ligand unbinding, reaction intermediates diffusing away, or visualizing conformational changes where certain parts detach or reposition.
However, until recently, such animations were often manually created—requiring precise positioning, scripting movements, and tedious adjustment. The Undock animation in SAMSON replaces this pain with a semi-automated, flexible feature that computes final positions and provides control through keyframes and parameter editing.
Getting started with Undock
Here’s how to begin using the Undock animation in your own project:
- Select your nodes first. Choose at least two atoms, molecular groups, or meshes in the SAMSON document. The first selection acts as the static receptor, and the rest will be animated away from it. If needed, group your receptor components in a folder and select that instead.
- Locate the animation. In the Animation panel of the Animator, double-click on the “Undock” effect.
- Adjust your keyframes. SAMSON creates an Undock animation between two keyframes by default. Move these keyframes to control when and how fast the undocking occurs.
- Fine-tune the movement. Although SAMSON computes the amplitude of undocking automatically, you can modify it anytime in the Inspector. For even finer control, you can also adjust the easing curve to change how parameters are interpolated during the animation.
A visual example
Here’s how the Undock effect can look in a molecular scene:
This example shows a molecular component gracefully separating from its receptor. The motion is smooth, the path is computed automatically, and the setup only takes seconds. Whether you’re preparing a visual for a paper, teaching molecular mechanisms, or building an interactive demo, this can save you serious time.
Useful tips
- If no nodes are selected, SAMSON will attempt to guess which ones are to be undocked. For precise results, always select your nodes manually.
- All animations are now accessible from the Animation panel, not the old Animation menu. Make sure you’re using the updated interface.
- If you’re applying Dock and Undock animations together, using folders to group static and mobile parts helps organize the process.
To explore more technical details, visit the full documentation page here.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON from https://www.samson-connect.net.