When preparing a molecular presentation, one common challenge is showing a group of atoms or a mesh moving into place while keeping the structure it approaches easy to compare against. A sudden jump between two views can obscure the relationship between the moving object and its surroundings. In SAMSON, the Dock animation can provide a simple visual transition: it keeps one selected node as the static receptor and animates the other selected nodes toward their current positions.
It is important to understand what this animation represents. Dock uses the selected nodes’ current positions as the docked positions, then automatically computes starting positions away from them. It is an animation for illustrating movement in a presentation; the documentation does not describe it as a molecular docking calculation or a method for finding a binding pose.
Choose the reference before you animate
Start by selecting at least two structural nodes or meshes in the document. The first selected node acts as the static receptor; the other selected nodes are animated. This makes selection order meaningful. If the receptor is made up of several nodes, put those receptor nodes in a folder and select the folder first. Select the group or mesh you want to move as well.
A useful pre-animation check is to ask: “What should stay still, and what should move?” Make the structure that should remain fixed the first selection, and make sure the moving structures are included too. This small check can prevent the confusing result of animating the reference instead of the object you meant to show. If nothing is selected, SAMSON will try to guess which nodes the animation should apply to, but selecting the intended nodes directly gives you a clearer setup.
Add the animation, then shape its timing
With the nodes selected, open the Animation panel in the Animator and double-click the Dock animation effect. The selected nodes are docked between the animation’s two keyframes. You can move those keyframes to change where the animation sits in your presentation timeline.
The movement amplitude is computed automatically when the animation is created. If the resulting motion does not suit your presentation, inspect the animation and change its amplitude in the Inspector. You can also modify the easing curve to change how the parameters are interpolated between frames. These controls are useful for adjusting the visual pacing: for instance, you might give viewers more time to see the separation before the moving structure reaches its docked position. The keyframes can be moved whenever you need to revise the timing.
A quick setup checklist
- Identify the receptor or reference structure that should remain still.
- Select it first. If it consists of multiple nodes, group them in a folder and select that folder as the first node.
- Select the structural nodes or meshes that should move.
- Add Dock from the Animator’s Animation panel.
- Review the automatically computed movement, then adjust amplitude, easing, or keyframe placement if needed.
This workflow is especially useful when the goal is to communicate a spatial relationship in an animation: viewers can see the moving group approach its designated position while the receptor remains a stable reference. For examples, the documentation links to presentations using Dock for 2AZ8 and 5SAT. To learn more about the setup and properties, see the Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.