A molecular scene can contain all the right structures and still be difficult to read. When a ligand, molecular group, or mesh begins in its final position, viewers may miss what is changing. Moving the pieces by hand can also make it harder to keep the receptor still and coordinate the animation. SAMSON’s Dock animation offers a straightforward way to create this kind of visual transition: it starts selected moving nodes away from their current positions and animates them back to those positions.
One important distinction: here, Dock is an animation effect. It moves groups of atoms or meshes for a presentation; the documentation describes no search for binding poses or calculation of molecular interactions. Think of it as a way to show a structure arriving at a chosen position—not a replacement for a molecular docking calculation.
Set up the receptor and moving parts
Before adding the animation, select at least two structural nodes or meshes in the document. The first selected node serves as the static receptor. The other selected nodes are animated. That ordering is the key to a predictable result: put the receptor first, then select the parts you want to see move.
If the receptor consists of several nodes, group those receptor nodes in a folder and select the folder as the first node. This lets multiple receptor components serve together as the stationary reference. The remaining selected nodes can then be the animated group or groups.
For a clear presentation, decide what should remain fixed and what should move before you create the effect. This simple planning step helps avoid a common source of confusion: accidentally treating a component you intended to animate as part of the receptor, or vice versa. If nothing is selected, SAMSON will try to guess which nodes the animation should apply to. When the intended roles matter, selecting them explicitly gives you more control.
Create the motion, then tune its timing
Open the Animation panel in the Animator and double-click the Dock animation effect. The selected moving nodes will be docked between the animation’s two keyframes. Their current positions are treated as the docked positions, while starting positions are computed away from them automatically.
This means you do not need to manually set up the animation’s starting positions. After the effect is created, move its keyframes as needed to fit the timing of your presentation. The movement amplitude is computed automatically when the animation is created; if you want to change how far the animated nodes travel, inspect the animation and adjust its amplitude in the Inspector.
Timing affects how the motion feels, even when the start and end positions stay the same. You can change how parameters are interpolated between frames by adjusting the animation’s Easing curve. For example, consider whether a gradual or more direct transition will make the sequence easier for your audience to follow. You can also reposition the keyframes later, so the animation can be fitted into a larger presentation without recreating it.
A practical check before presenting
- Confirm that the receptor is the first selected node—or that its folder is first if it has multiple components.
- Check that the intended moving nodes are also selected.
- Preview the transition between the two keyframes and inspect the amplitude if the movement needs adjustment.
- Adjust the keyframe positions and easing to make the motion fit the pace of the surrounding presentation.
These checks help keep the animation focused on the structural change you want to communicate, rather than on accidental movement or awkward timing. The Dock effect is especially useful when a presentation needs to show components approaching a position that you have already established in the model.
To see the complete instructions and related details, visit the SAMSON Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.