Many molecular modelers know the frustration: you load a ligand or protein into your modeling environment and need to align it properly in 3D space—maybe for comparison, maybe for analysis, or maybe just to organize a complex scene. But trying to align different structures manually, atom by atom or with imprecise movement tools, can be tedious and error-prone.
If you’re using SAMSON, there’s good news: the platform offers several straightforward ways to align structures precisely to the global reference frame. In this blog post, we highlight how to quickly center and align your molecular structures using built-in features available via context menus and visual widgets—no scripting required.
What is the Global Reference Frame?
In SAMSON, the global reference frame refers to the XYZ axes and associated XY, YZ, and XZ planes that define the spatial coordinate system of the scene. Aligning structures to this frame ensures consistency in positioning, which is crucial when comparing different molecular models or preparing publication-quality visualizations.
Aligning Structures in the Global Reference Frame
To begin aligning objects:
- Right-click on the molecular structure in the viewport or in the Document view.
- Select Move selection in the context menu.
- Choose one of the alignment options:
- Center on the origin
- Align with X / Y / Z axis
- Align with XY / XZ / YZ plane
Using these options, you can standardize orientations of multiple structures without manual repositioning. This is especially helpful when preparing a visual comparison or when exporting the scene for further processing.
Visual Aid: Enable the Grid
Having trouble recognizing the orientation of your models? You can enable the grid display in the bottom menu of the viewport to show the XY plane at Z = 0. This provides a visual reference to help confirm alignment actions.
Alternative: Using the Compass Widget
If you prefer a more tactile approach, SAMSON offers compass actions. Right-click on the visual compass widget located in the corner of the viewport to access alignment options. This is a fast way to align selected structures to the global frame without navigating menus.
When to Use This
Aligning structures is useful in many modeling workflows:
- Overlaying molecules to assess structural similarity
- Positioning components in an assembly before simulation
- Creating visually tidy scenes for presentations or publications
- Ensuring consistent input for data analysis or scripting
With these tools, you don’t need to rely on trial-and-error positioning or complicated scripting.
To learn more, visit the full documentation page on moving objects in SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.