When building, comparing, or preparing molecular models for visualization or simulation, one common issue faced by modelers is the orientation and relative positioning of molecular structures. Misaligned molecules can complicate analysis, generate cluttered views, and obstruct accurate measurements or transformations. Fortunately, SAMSON provides an intuitive way to align molecular structures using the global XYZ reference frame.
Whether you’re preparing a publication-quality render, analyzing docking results, or setting up a molecular assembly, realigning molecules in a consistent coordinate frame can improve readability, enable automation, and save time. Here’s how you can do that in SAMSON using built-in context menu options—no scripting needed.
Why align with the global reference frame?
The global reference frame in SAMSON defines the universal X, Y, and Z axes in your workspace. By aligning molecular structures with these axes or to specific planes (XY, YZ, XZ), you can:
- Compare molecules more easily side-by-side
- Control rendering angles for publication images or animations
- Simplify further alignment, measuring, or construction tasks
- Standardize coordinate systems for compatibility with other tools
How to align molecules in SAMSON
To align a molecule in SAMSON:
- Right-click on a structure in the viewport or click the current selection in the Document view
- Navigate to Move selection in the context menu
- Select one of the following alignment options:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, XZ, or YZ plane
You can combine multiple options (e.g., center and then align with the Z axis) to fully control position and orientation.
Visualizing the reference frame
Not sure where the global frame XY plane lies? Toggle on the grid from the viewport’s bottom menu. You’ll see the XY plane at Z = 0, which can help you position your structures more precisely.
Tip: Combine global alignment with snapping and move editors for maximum precision. For example, after aligning one molecule, you can precisely arrange others around it using the Global Move Editor.
Suggested workflows
- Structural comparison: Load two molecules, center them both on the origin, and align each one to a common axis. This lets you toggle between them or overlay them easily.
- Model assembly: Align fragmented components to planes or axes before using snapping and distribution tools to build larger structures.
- Export preparation: Ensure molecules are consistently oriented before exporting images, movies, or coordinate files for external tools.
This quick alignment feature is particularly useful for beginners who want clean, interpretable visuals, and for advanced users preparing for scripting, simulation, or publication.
To explore this and more object manipulation tools, visit the official SAMSON documentation: https://documentation.samson-connect.net/users/latest/moving-objects/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.