Animating molecular systems is a powerful way to communicate ideas, validate hypotheses visually, and produce engaging scientific presentations. Yet for many molecular modelers, creating such animations can feel out of reach, especially if it involves scripting or manual work frame by frame. If you’ve ever thought: “I just want to move a few atoms from A to B without spending hours,” then you might like what SAMSON’s Move atoms animation feature offers.
The Move atoms animation in SAMSON allows you to create smooth transitions of atoms between key positions without writing a single line of code. Using intuitive visual controls built into the Animator workspace, you can visually position atoms at different points in time and let SAMSON handle the interpolation. This is particularly helpful when showing docking motions, exploring conformational changes, or simply illustrating molecular dynamics in an accessible way.
Where to Start
To begin, select one or more atoms in your molecular system. Then go to the Animation panel in the Animator and double-click on Move atoms. This will create a starting keyframe at your current frame position.
Then, move the frame cursor on the timeline to your desired future frame. Use SAMSON’s 3D manipulation tools—such as Move editors or the Twister editor—to reposition your atoms. When you’re satisfied with the new configuration, simply add a second keyframe. SAMSON will automatically create a smooth 3D trajectory between both keyframes, resulting in a fluid animation between atom positions.
Editing and Refinement
Need adjustments? Keyframes can be repositioned any time by dragging them along the animation timeline. If you need to change the motion between keyframes, simply update the atomic positions and overwrite the keyframe.
Additionally, the animation’s properties can be fine-tuned using the Inspector panel. You can smooth motions using interpolators or apply different easing curves for more natural transitions. Make a molecule slow in the beginning, accelerate in the middle, and slow near the end—without writing code.
Beyond the Default
If the default controllers from the Move atoms animation aren’t flexible enough for your needs, you can temporarily disable them from the Document view and use other advanced editors. For example, the Move editors and Twister editor allow you to apply transformations like rotations or complex twisting motions. Once done, just add a keyframe and your animation sequence will include these changes seamlessly.
When Is This Useful?
The Move atoms animation is ideal when you want to:
- Demonstrate the motion of molecules during conformational change
- Present docking or assembly pathways
- Create schematic animations of custom interactions
- Show transitions between different calculated structures without trajectory files
Rather than calculating whole MD simulations or exporting frames to external software, you get control, clarity and speed – all within SAMSON.
To learn more, visit the full documentation page here: https://documentation.samson-connect.net/users/latest/animations/move-atoms/
SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON at https://www.samson-connect.net.