A molecular scene can contain the right structures and still be hard to explain. When a ligand or another group of atoms is already in its final position, viewers may not see how it relates to the surrounding structure—or what you want them to focus on. A carefully arranged docking animation can make that spatial relationship easier to follow.
In SAMSON, the Dock animation moves selected atoms or meshes from automatically computed starting positions toward their current positions, which are treated as the docked positions. It is a way to present a movement in a molecular scene. It does not, by itself, calculate a molecular docking pose.
Set up the receptor and moving structure
Before adding the animation, decide which structure should stay still and which structures should move. Select at least two structural nodes or meshes. The first selected node acts as the static receptor; the other selected nodes are animated. That selection order matters, so check it before creating the animation.
If the receptor consists of several nodes, you can group them in a folder and select that folder first. This gives the animation a single receptor selection while keeping the receptor components together in the document. If you leave nothing selected, SAMSON will try to guess which nodes the animation should affect. For a presentation where the roles need to be predictable, making the selection explicitly is the clearer approach.
Add the motion and place it in time
With the intended nodes selected, open the Animation panel in the Animator and double-click the Dock effect. The selected moving nodes will be animated between the two keyframes. Move those keyframes to choose when the motion begins and ends in your presentation.
The animation’s movement amplitude is computed automatically when you create it. If the resulting travel distance does not suit the scene, inspect the animation and adjust its amplitude. This is useful when a default movement feels too large for a close-up view, or too small to read clearly at the scale of the full molecular scene. You can also change the easing curve to control how animation parameters are interpolated between frames.
Use the motion to answer a viewer’s question
Before settling on timing and amplitude, consider what a viewer should notice. Is the goal to show a group approaching a receptor, to make the final arrangement easier to recognize, or simply to direct attention to a particular part of the scene? Keep the motion and timing in service of that explanation. A movement that is too brief may be difficult to follow; one that occupies too much of the presentation may distract from the structure itself.
It also helps to inspect the scene at both keyframes. The final frame should show the intended docked arrangement, since the current positions are used as the docked positions. The starting positions are computed automatically away from them. If you need to change the animation’s timing, the keyframes can be moved after creation.
One interface detail may differ from older demonstrations: animations are accessed through the Animation panel in the Animator, rather than the former Animation menu. Presentation actions are available through the Animator’s controls.
For examples of presentations using this animation, see 2AZ8 – Dock animation and 5SAT – Dock animation. To learn more about setup and properties, visit the Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.