When a molecular scene contains several separate components, the final arrangement may be easy to recognize—but hard to explain. Showing only the completed structure hides where the components began and how they come together. A Dock animation can make that transition visible, helping viewers follow the assembly without requiring a long verbal explanation.
In SAMSON, the Dock animation moves selected groups of atoms or meshes toward their current positions, which serve as the docked positions. The starting positions are computed automatically away from those positions. This makes the animation useful for presenting a before-and-after arrangement in a molecular scene.
Set the receptor and moving components
The selection order matters. Select at least two structural nodes or meshes, with the receptor first. The first selected node remains static; the other selected nodes are animated. For example, if you want to show several components approaching a receptor, select the receptor first and then select the components that should move.
If the receptor consists of multiple nodes, group them in a folder and select that folder as the first node. This gives the animation a single receptor selection while keeping its constituent nodes together in the document. If nothing is selected, SAMSON will try to guess which nodes the animation should affect, but an explicit selection gives you more control over what stays fixed and what moves.
Build the transition
With the intended nodes selected, open the Animation panel in the Animator and double-click the Dock effect. The selected nodes will be docked between the animation’s two keyframes. Move the keyframes as needed to place the transition at the right point in your presentation.
The movement amplitude is calculated when the animation is created. If the automatically chosen movement does not suit the scene, inspect the animation and change its amplitude. You can also adjust the easing curve to change how the animation parameters are interpolated between frames. These controls help you fit the transition to the story you want the presentation to tell: for instance, a short, direct move or a more gradual arrival.
A useful distinction when presenting results
Here, “Dock” describes an animation in a molecular scene: selected nodes move toward positions that are already represented in the document. The documentation describes how to animate that movement; it does not describe a search for binding poses or a method for evaluating whether a pose is scientifically favorable. Keeping that distinction clear helps viewers understand whether a figure is showing a computed result, a structural arrangement, or a visual transition.
A quick setup checklist
- Identify which node or folder should stay fixed and select it first.
- Select the groups or meshes that should move.
- Add Dock from the Animator’s Animation panel.
- Review the two keyframes and position them to fit the presentation.
- Inspect the movement amplitude and easing curve if the transition needs adjustment.
This small amount of setup can make a crowded molecular scene easier to read: viewers see which parts are stationary, which parts move, and where the components end up. For more details, see the Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.