Preparing molecular animations is a frequent task in structural biology, medicinal chemistry, and computational modeling. One challenge that often arises is how to visually present molecules as they dock into a receptor, making this interaction clear, educational, and even aesthetically pleasing. Whether your goal is to use the animation for a publication, a presentation, or an internal report, having precise control over molecular movements can be extremely beneficial.
Enter the Dock animation feature in SAMSON: a useful tool for animating how atoms or groups of atoms move into their final, ‘docked’ positions. This becomes especially valuable when you want to show a ligand approaching a protein receptor, or the self-assembly of molecular structures. Here, we’ll walk through the key steps and considerations, as well as how this simple tool can solve a real-world presentation challenge.
Why this matters
It’s difficult to communicate molecular binding or interaction just through static images. Dynamic animations help your audience understand both the result and the process. However, manually animating this kind of trajectory can be time-consuming and imprecise. The Dock animation automates much of this by calculating a start point for your atoms and interpolating the movement toward the receptor.
How to set it up in SAMSON
To begin, select at least two nodes or meshes: the first will act as the static receptor, while the others will be animated. If several objects need to serve as the receptor, create a folder, add those nodes to it, and select the folder first.
Once your selection is made, go to the Animation panel within the Animator and double-click the Dock animation. This will automatically place your animated atoms at starting positions away from the docking position and generate the animation between two keyframes.
Use the timeline to shift the keyframes as needed. This lets you control when the docking starts and stops during your presentation.
Controlling the docking effect
You might notice that some docking movements appear too subtle or too exaggerated. Fortunately, the amplitude of the docking animation is automatically calculated but can be adjusted in the Inspector. Whether you want a dramatic sweeping motion or a subtle nudge, tweaking the amplitude helps.
You can also adjust the easing curve to control how the atoms speed up or slow down between keyframes. This provides an additional layer of realism for your animations.
Quick tip: watch out for interface changes
Note that older SAMSON documentation might reference an Animation menu that no longer exists. All animations, including Dock, are now found in the Animation panel within the Animator: use Ctrl + 7 (or Cmd + 7 on Mac) to access it quickly.
Examples to explore
Want to see it in action? Check out these published examples created with SAMSON:
These real presentations show how the animation helps explain molecular mechanisms visually, without adding unnecessary complexity to your workflow.
To learn more, visit the official documentation page for the Dock animation: https://documentation.samson-connect.net/users/latest/animations/dock/
SAMSON and all SAMSON Extensions are free for non-commercial use. Learn more and get SAMSON at https://www.samson-connect.net