Visualizing molecular motion is crucial when designing presentations or exploring structural hypotheses in molecular modeling. One of the challenges often faced by modelers is effectively communicating the concept of molecular dissociation — for example, when an inhibitor unbinds from a protein pocket. These movements can be difficult to represent clearly, especially when you need to show the transition from a bound to an unbound state. This is where animation becomes particularly useful.
SAMSON provides an Undock animation feature that helps depict molecules or meshes separating from docking positions. Whether you’re preparing a lecture slide, a conference visualization, or a molecular design demonstration, this tool can help you generate smooth, interpretable animations directly from your structural models.
What does the Undock animation do?
The Undock animation creates an automatic motion where selected atoms or meshes “undock” — meaning they move away from their initial positions, which are interpreted as their docked states. SAMSON computes the final undocked positions automatically, saving you the trouble of manually adjusting coordinates.
This animation is particularly helpful when communicating events such as:
- Ligand departure from a binding pocket
- Subunit separation in a protein complex
- Detachment of a molecular fragment or nanostructure
Adding the Undock animation
To begin, simply select at least two structural nodes or meshes. The first selection acts as the fixed receptor, while all others become animated and will be undocked.
If multiple elements are to be treated as the receptor, place them in a folder and select that folder first. If no selection is made, SAMSON attempts to guess the appropriate target automatically.
Then, open the Animation panel in the Animator and double-click the Undock animation effect. The animation will be inserted between two keyframes by default. You can drag and reposition these keyframes to control the timing.
Tweaking motion properties
By default, the amplitude — or distance — of the undocking motion is generated automatically. However, this can be edited by inspecting the animation. In the animation’s properties, you can adjust movement amplitude to fit your presentation needs more closely.
Additionally, you can modify how animation parameters transition between keyframes using the Easing curve. This allows for more natural motion curves, depending on the context: smooth, abrupt, or even elastic transitions are possible.
Example in action
The image below shows an example of the Undock animation depicting ligand departure. You can preview such animations directly in SAMSON:
Part of a flexible animation system
The Undock animation is just one of several effects in SAMSON’s animation system. It pairs well with animations like Dock, Move atoms, and Hold atoms, offering a flexible set of options to communicate dynamic biological or nanotechnological processes.
You can learn more in the original Undock animation documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.