When constructing complex molecular systems, one common challenge modelers face is positioning fragments exactly where they should go. Whether you’re combining rings, functional groups, or biomolecular motifs, ensuring correct orientation can make or break your structure. Misplaced fragments can lead to non-physical models or wasted time reorganizing atoms.
The Local Move Editor in SAMSON addresses this pain point. It offers precision and interactive feedback for fine-tuning orientations of molecular fragments after insertion. Here’s how you can take advantage of this functionality to improve your modeling workflow.
Setting a Precise Rotation Pivot
Once you’ve inserted a fragment but find it’s not facing the desired direction, select it and press M to activate the Local Move Editor. By default, rotation occurs around the geometric center of your selection. However, you can choose any atom as your pivot:
- Zoom into the region of interest so the pivot atom is not obscured by the Move Editor’s sphere.
- Click directly on the atom you want to serve as the rotation center.
This gives you finer control—essential when placing fragments like sugar moieties, aromatic groups, or protecting units onto a larger molecule scaffold.
Interactive Rotation and Adjustment
Simply press and hold on the sphere’s surface and drag the mouse to rotate. You can use the colored arrows around the sphere to rotate along the three principal axes. All updates are shown in real-time.
In the following example from the documentation, a user orients an N-acetyl fragment on an α-D-galactopyranose derivative, carefully aligning it with the target connection point:
This method proves particularly helpful when modeling glycosylation, attaching fluorescent labels, or exploring rotational conformers within supramolecular systems.
Rotating Around Bonds
Beyond rotating whole fragments, you can rotate around a single bond—ideal for optimizing conformations. Switch to the Local Move Editor, then:
- Click the bond you want to rotate around.
- The editor automatically selects the smallest rotatable part and displays a rotary controller.
Watch this in action where a fragment is rotated precisely around a bond axis:
Snapping and Advanced Placement
When precision is critical, you can combine fragment orientation with snapping options. In the Viewport’s top-left corner, access translational and angular snapping controls. Align fragments on grids or at fixed angles—useful for crystalline materials or symmetric assemblies.
Bonus: Distribute and Align Structures
The Global Move Editor (shortcut K) expands on this by allowing larger-scale rotations and translations. Combined with snapping and pivot controls, it helps distribute repeating fragments or build supramolecular architectures with ease.
To learn more about using the Local and Global Move tools for fragment orientation, visit the full documentation page on Building Molecules in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.