Creating compelling molecular presentations isn’t just about showing beautiful structures — it’s also about helping your audience grasp what’s happening at the molecular level. One frequent need for structural biologists and molecular modelers is to present docking and undocking events, such as a ligand binding to or releasing from a receptor. Manually animating such events in molecular visualization software can be tedious, especially when repeating similar tasks across multiple systems or presentations.
To reduce that repetitive workload, SAMSON offers a useful tool: the Undock animation. It automates the process of moving atoms or meshes away from a receptor, giving a clear visual effect of a molecule disengaging from a binding site. This is particularly helpful when communicating structural rearrangements during molecular simulations, fragment screening processes, or just showcasing docked poses in a way that’s easier to understand visually.
Why the Undock Animation Saves You Time
If you’ve ever spent time keyframing coordinates by hand to show atoms leaving a binding site, you’ll appreciate how SAMSON handles this for you automatically. The undock animation starts with the docked configuration and computes a path for selected atoms or meshes to move away from it. The final position is determined algorithmically, meaning the animation provides a believable off-site position without any need to script or calculate exit paths.
Additionally, if you use multiple ligands or other atom groups, SAMSON lets you group receptors or other static elements using folders. It then treats the folder contents as a single reference frame — helpful when undocking multiple ligands from a multimer or complex binding pocket.
Steps to Use the Undock Animation
- Select at least two elements: the static part (e.g., receptor) and the part to be animated (e.g., ligand). If needed, use a folder to group receptor elements.
- Open the Animation panel available in the Animator interface (shortcut:
Ctrl+7orCmd+7). - Double-click the Undock animation effect. SAMSON will insert keyframes between which the undocking will happen.
- Adjust keyframes in the timeline if needed — you can change their timing to control animation speed or duration.
- To adjust how far the atoms move, open the Inspector and modify the amplitude value.
Fine-Tuning the Motion
The amplitude determines how far atoms move during undocking — useful for either a short release or a more dramatic separation. You can also control the interpolation of parameters between keyframes via an Easing curve, which adds natural acceleration or deceleration to the atoms’ motion.
What It Looks Like
If you’re curious about the visual result, here’s an example of the Undock animation in action:
Whether you’re preparing figures for a lecture or submitting a video abstract, the undock animation simplifies the preparation process by automating what typically requires quite a bit of manual work. It’s an understated yet surprisingly practical feature when you need to present clear molecular motions quickly.
Want to explore more? Visit the full documentation page here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.