When preparing a molecular presentation, a common challenge is showing where a group of atoms or a mesh belongs without manually arranging a convincing starting position first. The Dock animation in SAMSON can help: it treats the selected structures’ current positions as the docked positions, then automatically computes starting positions away from them.
One important distinction: this is a presentation animation. It moves selected nodes between positions; it does not, by itself, calculate a molecular docking pose or establish that a pose is scientifically valid. Choose the intended final arrangement before adding the animation.
Set up the receptor and the moving structure
Select 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 selection order matters. Before applying the effect, check that the intended receptor is first and that the structures you want to move are included in the selection.
If the receptor consists of multiple nodes, place those receptor nodes in a folder and select the folder as the first node. Select the moving nodes along with it. This gives the animation one receptor selection while letting the receptor be represented by several nodes.
If nothing is selected, SAMSON will try to guess which nodes the animation should apply to. For a presentation where the distinction between fixed and moving structures matters, explicit selection is the more predictable approach.
Create the motion from the intended final pose
With the relevant nodes selected, open the Animation panel in the Animator and double-click the Dock animation effect. The selected nodes will be docked between the animation’s two keyframes. Since their current positions are treated as docked positions, arrange the scene in the desired final state before creating the animation.
The starting positions are computed automatically away from the docked positions, and the movement amplitude is calculated when the animation is created. This saves you from having to place every moving structure manually just to establish the animation’s starting point. It also means that if the initial movement is not right for your presentation, you may need to adjust the animation rather than repositioning the receptor.
Refine the timing and distance
Move the animation’s keyframes as needed to control where the motion falls in the presentation. You can change the movement amplitude by inspecting the animation, and change how its parameters are interpolated between frames by adjusting the easing curve. These controls address different aspects of the result: amplitude changes the extent of the movement, while the easing curve changes how the animation progresses between frames.
A practical review is to play through the relevant section and check three things: does the intended receptor stay static, do the selected structures arrive at the intended positions, and does the timing fit the surrounding presentation? If the result needs adjustment, revisit the keyframes, amplitude, or easing rather than assuming the automatically computed starting positions are fixed.
Older recordings may show an Animation menu that is no longer present. In current SAMSON, animations are accessed through the Animation panel in the Animator, and presentation actions are available through the Animator’s controls.
For examples, the documentation links to presentations using Dock animation, including 2AZ8 – Dock animation and 5SAT – Dock animation.
For the complete instructions, see the Dock animation documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.