One of the most common needs in molecular modeling is to convey motion. Whether you’re presenting a molecular mechanism, visually inspecting orientation-dependent properties, or simply building educational or outreach material, showing the movement of molecular structures often works better than static images.
But rotational motion can be tricky. How do you rotate a group of atoms in a meaningful way — and not just spin it randomly in space?
Fortunately, SAMSON has a feature specifically for this: the Rotate animation effect. It lets you rotate any group of atoms around their centroid, along the Z-axis. This ensures that your animation remains centered and visually coherent.
Why it matters
Instead of showing a static structure, or rotating the entire view, you can now make precise rotations of specific parts of your molecular system. This enhances clarity when you’re, for example:
- Visualizing flexible domain motion (e.g. hinge movements)
- Presenting docking poses or alignment changes
- Explaining chirality or stereochemistry
- Creating rotations for 360° visualization on the web or in VR
How it works
Here’s how the Rotate animation works in SAMSON:
- Select your atoms: Begin by selecting the atoms (or molecules, or any group of particles) you want to rotate. This is typically done through the regular selection tools.
- Open the Animator: Open the Animator by going to the interface (you can use the shortcut
Ctrl + 7on Windows/Linux, orCmd + 7on macOS). - Double-click on ‘Rotate’: In the Animation panel, find the Rotate effect. Double-click it to apply it to the selected group. A pair of keyframes will define the rotation start and end.
- Adjust keyframes: Move the keyframes on the timeline to define when the rotation begins and ends. You can drag them to control the duration and timing.
The rotation is performed around a vector parallel to the Z-axis and passing through the geometric center (centroid) of the selected atoms. This keeps the rotation symmetric and visually clear.
Tweaking the motion
If you want to adjust how smooth or abrupt the rotation feels, you can change the Easing curve. This is especially helpful if you’re synchronizing multiple parts of a molecular animation or matching up with other visual cues.
Need to move the atoms differently?
This rotation is just one of several available animations. You might also want to explore the:
- Rock animation for back-and-forth motion
- Hold Atoms to freeze part of the molecule
- Move Atoms for more freeform movement
Example in action
Above is an example that uses the Rotate animation to smoothly rotate a selection of atoms. This simple animation can transform your molecular presentations into dynamic, informative visuals.
To learn more, head over to the full documentation page: https://documentation.samson-connect.net/users/latest/animations/rotate/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.