A molecular scene can be correctly arranged and still be difficult to explain. When you want to show a group of atoms or a mesh approaching a receptor, manually creating a convincing start position and transition can add unnecessary work—and can make it harder to keep the final arrangement exactly where you want it.
SAMSON’s Dock animation offers a presentation-focused way to build that motion. The positions already in your document are treated as the docked positions. When you add the animation, SAMSON automatically computes starting positions away from them. The animation then moves the selected nodes toward their existing destination.
Set up the receptor and moving group
Selection determines what stays in place and what moves. Select at least two structural nodes or meshes, with the intended static receptor first. The first selected node acts as the receptor; the other selected nodes are animated.
If your receptor consists of several nodes, group those receptor nodes in a folder and select the folder first, followed by the nodes or meshes you want to animate. This makes the intended roles clear: the folder is the stationary reference, and the remaining selected items move toward their docked positions.
A useful check before adding the animation is to ask: Is the destination arrangement already the one I want to show? Since the current positions become the docked positions, arrange the scene accordingly before creating the effect.
Add the animation and tune its timing
- Select the receptor and the nodes or meshes that should move.
- In the Animator’s Animation panel, double-click Dock.
- Review the resulting motion between the two keyframes and move the keyframes as needed.
- If the travel distance needs adjustment, inspect the animation and change its amplitude.
- To adjust how the animation’s parameters transition between frames, change its easing curve.
The movement amplitude is calculated automatically when the animation is created. That gives you a starting point without requiring you to set the distance first, while the Inspector lets you adjust it afterward. Keyframe placement controls when the motion occurs in your presentation; the easing curve controls how parameters are interpolated between frames.
When the result is not what you expected
If the receptor moves, check the selection order: the receptor must be first. If several receptor components should remain stationary, make sure they are represented by the folder selected as the first node. If the animated group ends in an unexpected place, check the nodes’ current positions: those are treated as the docked positions. If the motion feels too large or small, inspect the animation and adjust its amplitude.
If nothing is selected, SAMSON will try to guess which nodes the animation should apply to. For a predictable result, explicitly select the intended receptor and moving group instead.
Dock is useful when the goal is to communicate a transition into an arrangement you have already prepared. It creates an animation of movement; it does not replace the task of choosing and validating the molecular arrangement itself.
For the full instructions, see the Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.