When preparing a molecular presentation, it can be difficult to show how a group of atoms or a mesh relates to a receptor without moving the receptor itself. A static view may hide the spatial relationship; moving everything together can make it harder to follow what is changing. SAMSON’s Dock animation offers a simple way to animate selected groups toward positions they already occupy in the document.
One useful distinction: this is a presentation animation, not a molecular docking calculation. Dock treats the current positions as the docked positions and automatically computes starting positions away from them. The animation then shows the selected nodes moving between those positions. It helps communicate a spatial arrangement; it does not, by itself, determine or validate a binding pose.
Set up the receptor and moving group
Start by selecting at least two structural nodes or meshes. The first selected node acts as the static receptor; the other selected nodes are animated. That selection order matters. If the receptor consists of several nodes, put those receptor nodes in a folder and select the folder first, followed by the nodes you want to animate. This gives the animation a clear stationary reference while the other selections move.
If you have nothing selected, SAMSON will try to guess which nodes the animation should apply to. For a presentation where you need predictable roles, explicit selection is the clearer workflow: choose the receptor first, then the moving group, and check that both are included before adding the effect.
Add the animation and place it in the timeline
Open the Animator and find the Dock effect in its Animation panel. Double-click the effect to add it. The selected nodes will be docked between the animation’s two keyframes. Move those keyframes as needed to position the motion in your presentation.
The keyframes are useful for more than setting when the movement begins and ends. They let you fit the motion into the surrounding sequence. For example, you can place the animation after an introductory view of the receptor, then leave time afterward to inspect the resulting arrangement. The animation’s movement amplitude is computed automatically when it is created, so review the result in the context of the whole presentation rather than assuming the default timing or distance will suit every scene.
Refine the result
If the motion starts too far from the receptor or does not travel far enough for your intended view, inspect the animation and change its amplitude. You can also adjust the easing curve to change how animation parameters are interpolated between frames. These controls help you tune the visual transition without changing which node is the receptor or which nodes are animated.
A practical review checklist: confirm the receptor was selected first; check that the moving nodes are the intended ones; watch the transition between both keyframes; and adjust the amplitude or easing if the movement is difficult to follow. If you are showing multiple receptor nodes, verify that they are represented by the receptor folder selected at the start.
In current SAMSON, access animations through the Animation panel in the Animator. Older recordings may show an Animation menu that is no longer present. You can find the Dock documentation and related examples on the Dock animation page.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.