A molecular structure can be in the right place and still be difficult to explain. If you are preparing a presentation, a static image may show where a group of atoms or a mesh ends up, but not how it relates to the rest of the scene. The Dock animation in SAMSON helps make that relationship visible: it animates selected nodes from automatically computed starting positions toward their current positions, which are treated as the docked positions.
This is useful when the goal is to communicate a spatial arrangement, such as showing a ligand approaching a receptor in a presentation. It is important to distinguish this visual animation from a docking calculation: Dock animates nodes toward their existing positions; the documentation does not describe it as a method for predicting or optimizing a binding pose.
Set up the selection in the right order
The main source of confusion is often not the animation itself, but the selection. Before adding Dock, select at least two structural nodes or meshes. The first selected node is the static receptor. The other selected nodes are the ones that move. In practical terms, decide which part of the scene should remain fixed, then make sure it is first in the selection.
If the receptor consists of several nodes, group them in a folder and select that folder as the first node. This gives the animation a single receptor selection while keeping the receptor components together. The remaining selected nodes become the animated group. If you leave nothing selected, SAMSON will try to guess which nodes the animation should apply to; for a presentation where the roles matter, an explicit selection makes the intended setup clearer.
Add the animation, then place it on the timeline
- Select the receptor node or folder first, followed by the nodes or meshes to animate.
- In the Animator, open the Animation panel and double-click the Dock effect.
- Review the animation between its two keyframes, then move the keyframes to set when the movement starts and finishes in your presentation.
The selected nodes are docked between those keyframes. The movement amplitude is calculated automatically when the animation is created. If the initial separation does not suit your scene, inspect the animation and change its amplitude. You can also change the Easing curve to control how parameters are interpolated between frames.
A useful way to plan the result is to separate two questions: where should the animated group end up? and when should the audience see it move? The current positions define the destination; moving the keyframes changes the timing. Adjusting amplitude changes the extent of movement. Keeping these controls distinct makes it easier to refine a presentation without accidentally changing the intended final arrangement.
Check the result before presenting
After adding Dock, play the animation and confirm that the intended receptor stays still while the other nodes move. If the wrong part moves, revisit the selection order and check whether the receptor components should be grouped in a folder. If the motion is too large or too small, inspect the animation and adjust its amplitude. If the movement feels abrupt or gradual in the wrong way, try a different easing curve. You can move the keyframes whenever you need to fit the animation into the surrounding presentation.
These checks help make the animation easier to interpret: viewers can see which group is moving, what remains fixed, and where the movement ends. For examples of presentations using Dock, the documentation links to 2AZ8 – Dock animation and 5SAT – Dock animation.
For the complete instructions and animation properties, see the Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.