If you’ve worked with complex molecular assemblies, you know how frustrating it can be when your structures are all over the place. Whether importing files from different formats or manually building models, molecules can end up scattered in the viewport with inconsistent orientations. This not only looks messy—it also makes downstream analysis, rendering, and communication more difficult.
SAMSON’s Align Structures in the Global Reference Frame feature addresses this with a simple, clear set of options to bring order to your modeling environment. This blog walks you through how to align atomic structures to axes or planes of the world coordinate system with just a few clicks.
Why alignment matters
Consistent structure positioning is essential when you’re:
- Preparing input for simulations that assume a central reference system
- Creating clean visualizations for presentations or publications
- Designing multi-component systems where symmetry and relative positioning matter
- Exporting models to other software with coordinate system constraints
Align any structure in SAMSON
To align a structure in SAMSON:
- Select a molecule or group in the viewport or Document view.
- Right-click on it to open the context menu.
- Navigate to
Move selection, then pick the alignment option you need: - Center on the origin – move the centroid to (0, 0, 0)
- Align with X/Y/Z axis – rotate so your selection’s first principal axis lines up with one of the global axes
- Align with XY/XZ/YZ plane – ensure the structure lies flat on a main plane
This menu is streamlined and easy to access. It’s a small feature that solves a big pain point—especially useful when importing parts from different sources.
Use the grid for visual feedback
To make alignment clearer, enable the grid in the bottom menu of the Viewport. This shows the XY plane at Z=0, letting you instantly see if your object is resting on that plane or floating above/below.
Tip
You can quickly toggle the grid on and off for better spatial orientation.
When alignment is especially helpful
- Designing 2D layouts: Make membrane-bound molecules align with XY or XZ planes.
- Generating figures: Place structures consistently to make overlays and comparisons easier.
- Exporting for simulation tools: Make sure your systems are centered and well-oriented within bounding boxes.
Take advantage of these quick actions to save yourself time—and avoid frustration—during model preparation.
To learn more about structure alignment and other object manipulation techniques, visit the full documentation page: Moving Objects in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.