Many molecular modelers and structural biologists face a recurring challenge: how to clearly communicate docking processes in presentations or teaching materials. Static images often fall short when trying to illustrate the journey of a ligand towards its receptor. Wouldn’t it be helpful to show that movement — the actual docking — from an intuitive, visual perspective?
The Dock animation in SAMSON offers a simple way to animate this process. Whether you’re building a presentation for a paper, a lecture, or a group meeting, this can help you bring clarity to your molecular scenes — without scripting or external video tools.
What the Dock Animation Does
The Dock animation moves selected atoms or meshes toward predefined docked positions. In SAMSON, the current positions are considered their final docked positions — so the animation engines compute starting positions that move the atoms or meshes from further away into their destinations. This offers a clean and repeatable way to illustrate binding events or structural transitions.
When You Might Use It
- To demonstrate molecular docking mechanisms visually in your presentations
- To illustrate protein-ligand interactions dynamically in your teaching materials
- To prototype ideas about binding without complex docking simulations
Using the Dock Animation
Here’s how to start:
- Select at least two structural objects (nodes or meshes) in your SAMSON document.
- The first selected node will act as the receptor (static); the others will be animated to dock toward it.
- If you want multiple nodes to be the receptor, put them into a folder and select the folder as the first node.
- Then, double-click on the Dock animation effect in the Animation panel of the Animator.
You can adjust your animation by moving keyframes to define when docking begins and ends. The movement amplitude (i.e., how far the objects move) is computed automatically but can be tweaked in the Inspector. You can also modify the easing curve to control how fast or slow the docking happens over time.
Troubleshooting Tips
If you don’t select anything before applying the animation, SAMSON will try to guess what to animate. For more specific control, always make your selections clear first.
Also, note that the interface shown in older movies has changed slightly — all animation effects are now accessible via the Animator’s Animation panel (Ctrl+7 or Cmd+7).
See It In Action
This brief GIF illustrates a ligand docking into a receptor using the Dock animation effect. It’s a simple way to communicate a complex process visually.
Examples for Inspiration
Looking for real document examples that use this animation? Check out:
This approach saves time and offers viewers a natural grasp of your molecular system’s dynamics.
To learn more about the Dock animation and additional functionality, visit the full documentation page: https://documentation.samson-connect.net/users/latest/animations/dock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.