When preparing a molecular presentation or animation, communicating docking—how molecules or fragments fit together—is often more than just showing two structures side by side. A static image of a docked complex may be clear to experienced modelers, but lacks the visual impact and explanatory power of a dynamic docking motion. That’s where the Dock animation effect in SAMSON becomes a powerful tool for molecular modelers.
Rather than manually animating atoms or relying on pre-rendered motion paths, the Dock animation effect does the heavy lifting by intelligently moving groups of atoms or meshes toward a target receptor position. This helps present the final docked conformation, starting the motion automatically from a position calculated away from the docked pose.
Why It Matters
If you’ve ever needed to:
- Explain how a ligand binds to a receptor
- Show the docking result from a simulation run or database search
- Present structural changes over time during a docking process
… the Dock animation simplifies this visually. It removes the complexity of defining start and endpoints manually and focuses on clarity and movement.
How It Works
To create a Dock animation:
- Select two or more structural nodes. The first node acts as the static receptor. You can also choose a folder to group several nodes as the receptor.
- Then, double-click Dock in the Animation panel inside the Animator.
- The other nodes will animate toward the receptor from computed start positions.
You can still manually move keyframes to adjust timing, or inspect the effect to change properties like the amplitude of movement.
Customization Options
Two settings give you additional flexibility:
- Amplitude: Automatically calculated based on geometry, but editable if you’d like a shorter or longer motion.
- Easing Curve: Modify the interpolation between keyframes to create smooth acceleration or deceleration along the path.
This approach is particularly helpful when showcasing how molecules interact in educational presentations, video summaries, or when publishing visuals for reports and articles. Instead of flipping through static frames, the viewer gets to see how things happen, which can improve understanding significantly.
Example Use Cases
The Dock animation has already been featured in examples you can explore on SAMSON Connect, such as:
By combining clarity, clarity of intent, and minimal input, the Dock animation in SAMSON saves valuable preparation time and makes molecular interactions easier to share and understand.
To learn more about the Dock animation feature in SAMSON, 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 here: https://www.samson-connect.net