When a molecular scene contains several structures, a motion sequence can be hard to read: which structure is the reference, and which one is supposed to move? If the receptor shifts along with the molecule you want to animate, viewers may lose the frame of reference. SAMSON’s Dock animation offers a straightforward way to make the intended relationship clearer in a presentation.
Dock is an animation effect, not a molecular docking calculation. It creates a visual transition: selected groups of atoms or meshes move toward positions that are treated as docked positions. Their starting positions are computed automatically away from those positions. This can help you show a structural arrangement in a presentation, but it does not, by itself, predict or validate a binding pose.
Choose what stays still before you animate
The key to a legible result is the selection order. Select at least two structural nodes or meshes, with the intended static receptor first. The first selected node acts as the receptor; the other selected nodes are animated. In practical terms, pause before applying the effect and check that the reference structure is first in the selection.
If more than one node should make up the receptor, group those receptor nodes in a folder and select that folder first. This keeps the reference side of the scene together, while the other selected nodes can move. If nothing is selected, SAMSON will try to guess which nodes the animation should affect. That may be convenient when exploring, but for a presentation where the roles matter, an explicit selection is easier to verify.
Build the motion, then tune the timing
Once the intended nodes are selected, open the Animation panel in the Animator and double-click Dock. The selected nodes are docked between the animation’s two keyframes. Move those keyframes as needed to place the movement in the right part of your presentation.
The movement amplitude is calculated automatically when the animation is created. If the displacement feels too large or too small for the story you want the scene to tell, inspect the animation and change its amplitude in the Inspector. You can also adjust the Easing curve to change how parameters are interpolated between frames. These controls affect how the transition is presented; they do not establish whether the final molecular arrangement is scientifically correct.
A quick review before sharing
- Is the receptor first? Confirm that the first selected node—or folder of receptor nodes—is the part that should remain static.
- Are the moving structures selected too? Dock requires at least two structural nodes or meshes for an explicit selection.
- Does the transition fit the presentation? Check the keyframe placement and adjust the amplitude if the motion is distracting or difficult to see.
- Is the message clear? Treat the animation as a visual explanation of a pose or arrangement, not as evidence that a docking calculation has occurred.
Being precise about the selection and the animation’s purpose helps viewers focus on the structural relationship rather than guessing what moved or why. For the full setup instructions and related examples, see the Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.