Producing clean, precise animations of molecular motions is a common challenge in molecular modeling. Whether you’re preparing an academic presentation, building an educational resource, or visualizing a simulation outcome, controlling how atoms move from one conformation to another can be crucial to communicating your discoveries effectively.
In SAMSON, the Move atoms animation was designed specifically to help users interpolate atom positions over time for elegant, data-driven molecular presentations. You don’t need scripting or plugins—just a few well-placed keyframes.
What is the Move atoms animation?
The Move atoms animation allows atoms to move freely from one position to another across multiple keyframes. Instead of showing an abrupt change or forcing transitions, it interpolates atom positions smoothly, creating realistic transitions. This comes in handy when illustrating conformational changes, transitions during docking animations, or custom structural deformations.
A simple workflow for moving atoms
- Position and select the atoms you want to animate.
- Open the Animation panel in the Animator.
- Double-click the Move atoms effect to insert a keyframe at the current position.
- Move to a different frame of the animation track and reposition the atoms using either the Move atoms controller or other transformation editors (like the Move editors or Twister).
- Add another keyframe to lock the new position.
The result: the system will interpolate atom movements across the keyframes to produce smooth animations. If needed, you can adjust timing or delete keyframes by right-clicking a keyframe in the Animator’s Track view.
Fine-tuning your animations
SAMSON gives you flexibility to control interpolation details through the Inspector panel. Here you can edit easing curves and toggle smoothing effects to better match your motion intent. This feature is particularly helpful when specific acceleration or deceleration effects are needed to mimic realistic motions.
Combining transformations
If you prefer to manipulate positions with greater degrees of freedom, consider temporarily hiding the Move atoms animation controllers from the Document view. This enables the use of alternate editors such as the Twister for rotational changes. Once transformations are applied, simply add a keyframe to lock them in.
Use cases: animations that educate
Animations prepared with this approach don’t just look smoother—they help viewers understand dynamic behavior. From nanotube rotations to conformational changes, a few well-placed keyframes can make the difference between a static image and an engaging visual story.
To explore examples and apply these tools to your next project, visit the official documentation: Move atoms animation in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON from https://www.samson-connect.net.