Have you ever needed to prepare a molecular animation to illustrate how a ligand unbinds from its receptor? This step, while seemingly simple, is often time-consuming and prone to inconsistencies. Whether you’re creating a teaching video, preparing a conference talk, or writing a paper, smoothly demonstrating molecular unbinding can be surprisingly tricky.
The Undock animation in SAMSON offers a quick alternative: it automatically moves selected atoms or meshes away from their current (“docked”) positions in a way that clearly communicates unbinding or dissociation events. Think of it as an expressive “reverse docking” mechanism without needing to manually animate each step or compute energy profiles.
What is the Undock Animation?
The Undock animation enables you to present dissociation processes by automatically moving selected parts – like ligands or molecular fragments – away from a receptor. With just a couple of clicks, SAMSON lets you specify what should remain static (receptor) and what should move away (ligand or fragment). The final undocked position is automatically determined, ensuring that molecules move clearly apart for visualization purposes.
This is especially useful for:
- Creating educational content to visualize molecular interactions
- Communicating ideas in pitches or presentations
- Quick prototyping of binding and unbinding animations
Setting It Up: A Brief Guide
Here’s how to get started with the Undock animation in SAMSON:
- Select nodes in your document. The first node will serve as the receptor (static), and others will be the mobile parts (e.g., ligands).
- If the receptor consists of multiple nodes, group them into a folder and select that folder as the first object.
- Double-click the Undock animation effect in the Animation panel inside the Animator.
- Adjust the keyframes to control the timing of the animation.
- Use the Inspector to modify properties such as the amplitude (how far fragments move), or fine-tune transitions with the easing curve.
Important: If you don’t select anything, SAMSON will try to guess the participating nodes. That said, selecting explicitly will offer you more control.
Why It Matters
In daily molecular modeling work, the need to illustrate dynamic processes often falls into one of two categories: either it’s very rough and conceptual, or very precise and energy-based (e.g., MD simulations). The Undock animation bridges the gap. It’s ideal when:
- You need a clear, visual depiction of dissociation without simulation overhead
- You want more impact in visual materials without hours of manual keyframing
- You’re exploring hypothesis-driven rearrangement scenarios
Tips
- The easing curve allows for smooth, natural movement – ideal for making animations look more realistic or stylized depending on your needs.
- You can move keyframes at any time to re-time the animation without having to redo it.
Need inspiration? Explore actual SAMSON documents showcasing undock/dock dynamics in public repositories.
To learn more about configuring and customizing the Undock animation, refer to the full documentation here: Undock Animation Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.