Animating molecular models can often feel like trying to get a group of cats to dance in formation. You know the perfect conformational shift, the right torsion, the intended final position — but getting from frame A to frame B often involves clunky transitions or manual repositioning that takes forever.
This is where SAMSON’s Move atoms animation effect can save time and smooth out the workflow. If you’re creating molecular presentations or trying to visualize dynamic conformational changes, this tool gives you a simple way to interpolate the positions of atoms across keyframes. No scripting. No debugging.
How it works
To create an animation where a group of atoms moves across several frames, just:
- Use the selection tool to choose the atoms that should move.
- Double-click on Move atoms in the Animation panel of the Animator to create the first keyframe.
- Scroll to a different frame, reposition the atoms using either the built-in controllers or another transformation editor (like the Move editors), and a new keyframe is automatically added.
As you add these keyframes, SAMSON interpolates the atom positions between them, creating smooth transitions over time.
Keyframe control
Each keyframe you add is editable: you can shift them around in the animation timeline to adjust the pacing, or remove them by right-clicking in the Animator’s Track view and choosing Remove keyframe.
Don’t want the default trajectory? Control how transitions behave using easing curves and smoothing options. For example, you can speed up the transition at the beginning and slow it down at the end, which is great for simulating natural biomolecular motion.
Bonus: use multiple editors
This effect is also flexible. You can switch to other editors during animation setup. For example, turn off the Move atoms animation controllers temporarily in the Document view and move atoms using the Twister editor before setting a new keyframe.
When it helps most
Here are a few real cases where this feature can make your life easier:
- Simulating the step-by-step motion of atoms near a binding site.
- Creating a clean intro for a molecular visualization presentation by showing parts of a molecule moving into place.
- Exploring conformational changes that are hard to explain with static images alone.
If you’re curious to see examples, check out these public SAMSON Connect documents that use this feature:
Learn more in the full documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.