If you’ve ever had to manually position molecules or meshes into a pre-defined structure for visual presentations or structural studies, you know how tedious that process can be. This is especially true in molecular modeling, where visual clarity can make or break the interpretation of the systems you’re working on. The Dock animation in SAMSON offers a simple yet powerful solution to this repetitive task by automating the smooth movement of atoms or meshes directly into their desired positions.
Let’s walk through how this animation works and how it can help improve both your workflow efficiency and the quality of your presentation.
What is the Dock Animation?
The Dock animation effect allows selected groups of atoms or mesh objects to glide into specific positions — considered their ‘docked’ states. SAMSON automatically computes the starting points for these objects, placing them away from the docking positions to create a clean, visual transition.
This is particularly useful when you’re showcasing molecular binding events, assembling complex structures from subcomponents, or preparing engaging educational animations.
How to Add the Dock Animation
To use this animation:
- Select at least two nodes or meshes in your document. The first element will be treated as the static receptor (e.g., a protein), and the others will be animated (e.g., ligands).
- If you want multiple objects to act as the static structure, place them in a folder and select that folder as the first item.
- Then, go to the Animation panel in the Animator and double-click on Dock.
The animation is added between two keyframes. You can reposition these keyframes to control the timing of the movement. You may also inspect the animation to adjust the amplitude of the motion.
Example of a Dock animation showing molecules snapping into position.
Customization Options
SAMSON makes it easy to fine-tune the behavior of this animation:
- Amplitude: Change how far the atoms travel initially by editing the animation’s properties via the Inspector.
- Easing Curve: Control the speed profile between keyframes — for example, make the movement start slow and finish fast, or stay constant.
Common Use Cases
The Dock animation has been applied in several shared molecular presentations, such as:
Use these as inspiration when preparing your own molecular assemblies or educational content.
The Dock animation blends form and function, helping molecular modelers communicate spatial relationships clearly while saving time. If you’re finding yourself repetitively snapping components into place or needing better visual flow in your animations, this is an effect well worth trying.
To learn more about this feature, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/dock/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.