When preparing molecular animations or presentations, it’s often important to convey structural dynamics in a clear and intuitive way. A common need is to rotate a specific part of a molecule—like a ligand, domain, or fragment—around its own center, rather than around a global axis. This is particularly relevant when visualizing conformational changes or isolating the motion of a substructure.
If you’ve ever had to manually tweak rotation parameters or struggled to define a pivot point, you’ll appreciate how straightforward this becomes in SAMSON using the built-in Rotate animation. This feature allows you to rotate any selected group of particles around their geometric center, using a rotation vector aligned with the Z-axis.
Why Rotate Around the Centroid?
Often, molecular structures are positioned within a larger complex. If you rotate them around a fixed external point, the movement may look unnatural or lead to confusing overlaps. In contrast, rotating a selection around its own centroid keeps the motion localized and easier to follow. It also allows a more accurate depiction of component flexibility—for example, showing how a protein domain twists or how a small molecule orients during binding.
How It Works in SAMSON
To apply the Rotate animation in SAMSON, follow these steps:
- Select the group of atoms or particles you’d like to animate. Make sure the selection reflects a coherent part of the molecule whose motion should be isolated.
- Open the Animation panel from the Animator interface.
- Double-click on Rotate to apply the effect. A rotation animation is created between the current keyframe and the next one.
- You can adjust keyframes and change the rotation duration or smoothness using easing curves.
This lets you easily animate motions like a ligand spinning in its binding pocket, or a domain pivoting around a connector—critical when illustrating mechanisms of action or visualizing simulation results.
Does the Axis Always Point Up?
Yes. The Rotate animation uses the Z-axis (pointing “up” in the SAMSON viewer) as the axis of rotation. This simplifies the effect and ensures consistency. Combined with the ability to freely move and reframe keyframes, this makes the creation of coherent animations less tedious.
Example Animation
Here is a visual example of the Rotate animation in action:
In this example, a substructure rotates smoothly around its centroid across the animation keyframes. You can easily control how fast or how far it turns simply by adjusting the keyframe placements and the parameters in the Animator.
A Note About the Interface
Some older tutorials might reference a now-deprecated “Animation” menu. This has been replaced by a more intuitive interface through the Animation panel accessible via Animator (shortcut: Ctrl+7 or Cmd+7).
To learn more about the Rotate animation in SAMSON, visit the official documentation: https://documentation.samson-connect.net/users/latest/animations/rotate/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.