A molecular complex can be difficult to explain when every component occupies the same small region of the view. A receptor and its bound partners may be structurally clear, yet their relationship is hard to see at a glance. Moving components apart in a presentation can make the arrangement easier to follow—without changing the underlying question you are trying to communicate.
In SAMSON, the Undock animation creates a transition that moves selected atoms or meshes away from their current, docked positions. It is useful when you want to show what is grouped together in a complex, distinguish a receptor from its partners, or give viewers a clearer view of components that overlap. Think of it as a presentation aid: the animation illustrates spatial separation; it does not, by itself, establish that a molecular dissociation is physically plausible.
Set up the selection with the receptor first
Before adding the animation, select at least two structural nodes or meshes. The first selected node acts as the static receptor; the other selected nodes are animated. That order matters. If you want one protein to remain in place while a ligand or another component moves away, make the protein the first node in the selection.
If several nodes should remain together as the receptor, put those nodes in a folder and select that folder first. This gives you a practical way to treat a group as the stationary side of the animation, while selecting the components to move after it. If nothing is selected, SAMSON will try to guess which nodes the animation should apply to, but an explicit selection makes the intended roles easier to control.
Create and refine the motion
Open the Animation panel in the Animator and double-click the Undock animation effect. The selected nodes will be animated between two keyframes. You can move those keyframes to adjust when the separation happens in your presentation.
The movement amplitude is computed automatically when the animation is created. If the result is too subtle or too large for the view you want, inspect the animation and change its amplitude in the Inspector. You can also adjust the easing curve, which changes how the animation parameters are interpolated between frames. These controls help you tune the visual pacing and extent without rebuilding the selection from scratch.
A quick checklist before presenting
- Confirm the roles: the first selected node or folder should be the part you want to keep static.
- Check the moving group: the other selected nodes are the ones that will be animated.
- Review the amplitude: use the Inspector to make the separation clear without pushing components farther apart than your explanation needs.
- Place the keyframes: move them to fit the pace of the presentation.
- Keep the interpretation clear: describe the motion as a visual separation unless you have separate evidence for a physical process.
One interface detail is worth noting: older recordings may show an Animation menu that is no longer present. In current SAMSON, access animation effects through the Animation panel in the Animator, and use the Animator controls for presentation actions.
For related ways to animate molecular components, see Dock, Hold atoms, and Move atoms. For the full setup and property details, learn more in the Undock documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.