Designing molecular animations often involves illustrating dynamic structural changes, such as docking and undocking interactions between molecules. When preparing presentations, tutorials, or simulations for teams or publications, manually separating complex molecular interactions frame-by-frame can become repetitive and imprecise. SAMSON’s Undock animation offers a convenient solution to automate this part of your workflow.
The Undock animation in SAMSON gently moves selected atoms or meshes away from a reference structure, mimicking the undocking of a ligand from a receptor, for instance. This effect is commonly used to show how molecular components separate in presentations or educational material. Here’s what makes it especially useful:
When You Might Need It
Many molecular modelers make presentation slides or animations that include steps like visualizing a small molecule disengaging from a protein target. Doing this manually means moving objects, repositioning views, and exporting frames – multiple times. The Undock animation automates this in combination with SAMSON’s keyframe system.
How It Works
To apply the Undock animation in SAMSON:
- Select one or more atoms, groups of atoms, or meshes to undock.
- If you select multiple items, the first by default is considered the “static receptor,” and others are undocked relative to it.
- If your receptor comprises several objects, group them into a folder and select the folder first.
- Then, go to the Animation panel located in the Animator interface, and double-click the Undock effect.
This places an animation between two keyframes. The undock movement is generated automatically — no manual frame dragging required. You can fine-tune the timing by adjusting the keyframe spacing. SAMSON also provides options to change the movement’s amplitude via the Inspector.
Customize the Feel of the Motion
If you want a more natural motion (e.g., slow start and fast finish), adjust the easing curve. Linear movement, ease-out, and bounce-like transitions can all help emphasize different scientific messages.
Common Use Case: Ligand Unbinding
Imagine showing how a ligand undocks from a binding pocket. With Undock, set the ligand group as the animated node and the protein structure as the receptor. Then use the animation to illustrate the spontaneous motion of unbinding — viewers can better understand the spatial tunnel or path of egress. Great for posters, slides, or grant visuals.
Watch It in Action
Start Automating Your Visuals
You can combine Undock with other animation steps such as Holding atoms or Moving atoms to create sequences. Once complete, animations can be rendered or exported for video or online viewing.
To learn more, visit the official documentation: Undock Animation Documentation Page.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.