Creating clear and compelling molecular animations can be a challenge—especially when attempting to illustrate large-scale rearrangements, such as ligand binding or the docking of molecular fragments. For many molecular modelers, one of the recurring pains is the tedious manual adjustment of molecular positions across keyframes to convey docking behavior effectively.
If you are looking to demonstrate a docking process in your molecular presentation, the Dock animation in SAMSON offers a streamlined alternative. Instead of moving atoms manually, this feature automates the animation of molecules transitioning from an arbitrary starting point to a final, “docked” structure, making presentations smoother and more time-efficient.
What does the Dock animation do?
The Dock animation automatically moves selected atoms or meshes into their “docked” positions—meaning their current positions in the SAMSON document—while computing start positions away from their targets. This provides a smooth, visually meaningful transition that mimics the docking process without requiring any scripting or external files.
How to apply it?
Using the Dock animation is straightforward. Here’s a typical workflow:
- Select nodes or meshes: Choose at least two structural nodes in your document. The first selected node will act as the receptor (it remains static), and the remaining nodes will move into position.
- Apply the effect: Open the Animation panel in the Animator, and double-click on the Dock animation.
- Adjust the keyframes: You can move the keyframes to customize when the docking transition begins and ends in the animation timeline.
Customizing the Dock animation
The amplitude, or the distance from which the atoms begin moving towards their docked positions, is generated automatically. However, you can inspect and adjust this parameter later using the Inspector.
Additionally, if you want to fine-tune how the movement accelerates or decelerates, you can modify the Easing curve. Linear, ease-in, and ease-out transitions ensure the movement feels natural for different presentation styles.
Simple Example
The result of applying the Dock animation can be seen in this example:
When is this useful?
This animation is especially helpful when creating presentations to:
- Demonstrate ligand-receptor binding
- Model protein-protein or domain docking events
- Visually prepare animations for educational or communication purposes
Experimenting with this feature allows for rapid creation of dynamic molecular visuals that better communicate structural relationships and interactions.
To learn more and get started, visit the official documentation page: https://documentation.samson-connect.net/users/latest/animations/dock/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.