From scattered structures to a clear docking story

A molecular scene can contain the right structures and still be hard to read. When two or more groups begin far apart—or the starting arrangement is visually cluttered—it may be unclear which group is meant to approach which. Manually positioning every animated structure can also take time. SAMSON’s Dock animation offers a direct way to create that visual transition: it moves selected groups from automatically computed starting positions toward their current positions.

First, decide what the scene should communicate

Dock is a presentation animation, not a docking search. The positions your structures occupy when you create the animation are treated as the docked positions. SAMSON computes starting positions away from those positions, then animates the selected moving groups toward them. In other words, prepare the final arrangement you want to show before adding the animation.

This distinction matters when preparing a scientific presentation: the animation illustrates movement between positions, but it does not establish that a pose is energetically favorable or predict a binding mode. Use it to communicate a chosen structural arrangement, and use appropriate modeling methods to determine or validate that arrangement.

Set up the selection with the receptor first

Select at least two structural nodes or meshes. The first selected node serves as the static receptor; the remaining selected nodes are animated. Selection order is therefore part of the setup, not a cosmetic detail. Before adding the effect, check that the intended receptor is first and that the groups you want to move are included after it.

If the receptor consists of several nodes, place those receptor nodes in a folder and select the folder first. This gives the animation one receptor selection while keeping the separate structures together. For a predictable result, explicitly select the nodes rather than relying on SAMSON to guess which nodes should be animated when nothing is selected.

Add the animation, then tune its timing

1. Select the receptor and the groups or meshes to animate, in the correct order.
2. In the Animator, open the Animation panel and double-click the Dock effect.
3. Review the resulting animation and move its keyframes to set when the movement begins and ends.
4. If the movement distance needs adjustment, inspect the animation and change its amplitude in the Inspector.
5. Adjust the easing curve if you want to change how parameters are interpolated between frames.

The amplitude is computed automatically when the animation is created, so it is a useful starting point rather than a fixed final setting. Keyframes can be moved after creation, which helps you fit the motion into the pacing of a larger presentation. For example, you can give viewers time to examine the initial arrangement before the approach begins, or leave time afterward to inspect the docked scene.

A quick review before presenting

• Is the final arrangement correct? The current positions become the docked positions.
• Is the receptor first? The first selected node stays static while the other selected nodes move.
• Are all intended moving groups selected? Add any missing nodes or meshes before creating the effect.
• Does the movement read clearly? Adjust amplitude, keyframes, or easing if needed.

These checks help avoid a common presentation snag: a technically valid animation that moves the wrong group, or moves it at a pace that makes the scene difficult to follow.

To see the full instructions and related animation options, learn more in the Dock animation documentation.

Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.