Easing Ligand Unbinding Presentations with the Undock Animation in SAMSON

Visualizing molecular dynamics can be complex, especially when presenting ligand-receptor interactions to collaborators or students. A common challenge for molecular modelers is how to clearly and convincingly show a ligand leaving its binding site, without manually specifying precise atomic trajectories.

This is where the Undock animation in SAMSON can help. Designed for simplicity and clarity, the Undock animation automatically computes final positions for your molecules—away from their docked state—enabling meaningful visual storytelling with minimal manual setup.

What Does the Undock Animation Do?

The Undock animation effect in SAMSON moves selected atoms or structural meshes from their docked positions to undocked positions, which are computed automatically to simulate unbinding. This makes it ideal for illustrating processes such as ligand dissociation, subunit separation, or domain detachment during presentations or tutorials.

Why Use It?

Crafting a believable unbinding motion by hand can be tedious and error-prone. The Undock animation removes guesswork by automatically determining a direction and distance that separates molecules smoothly. This is especially useful when preparing animations for slides, articles, or interactive teaching materials where visual flow matters.

How to Use the Undock Animation

Here is a quick step-by-step overview to use the Undock animation in SAMSON:

  1. Select two or more nodes or meshes: The first item acts as a static receptor, while the others will be animated away from it. If you want multiple objects to act as the receptor, group them into a folder and select that folder first.
  2. Apply the animation: Open the Animator panel (using Ctrl+7 / Cmd+7), then double-click on the “Undock” animation effect. The animation will be created between two keyframes.
  3. Adjust the animation timing: Move keyframes to change when unbinding starts or stops. You can also customize the interpolation using different easing curves for more natural motion.
  4. Modify parameters: To increase or decrease the amplitude of the movement, open the Inspector panel and fine-tune the parameters of the Undock animation.

Best Practices and Tips

Here are a few helpful considerations while using the Undock effect:

  • If unsure what to select, SAMSON can try to assign roles automatically, based on context.
  • You can always reposition keyframes later to speed up or slow down the animation.
  • If you had previously used the old Animation menu (now deprecated), you can find all animation effects—including Undock—via the Animator panel.

Visual Example

Example: the Undock animation

This animation shows a ligand separating from its receptor automatically, without manual trajectory input. It’s especially useful to illustrate the final stage of a molecular docking study or to explain mechanistic models intuitively.

Applications Beyond Ligand Unbinding

While the Undock animation is ideal for ligands leaving receptors, it can also visualize detachment of protein subunits, separation of DNA strands, or even visualization of artificial constructs unzipping or expanding. Combined with the Dock, Move atoms, and Hold atoms animations, you can narrate complete conformational transitions.

Learn more and explore advanced usage in the full documentation: 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

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