If you’ve ever worked with complex molecular arrangements, you know how easy it is to end up with atoms scattered all over your viewport. Whether you’re preparing a clean scene for publication, building a supramolecular assembly, or simply organizing a structure before simulation, aligning molecular components precisely is a tedious but essential task.
Fortunately, SAMSON makes alignment straightforward with a set of built-in tools designed precisely for this purpose. In this post, we’ll focus on how to quickly align atomic structures within the global XYZ reference frame and distribute them in space using menu commands, compass tools, and snapping features — all inside the SAMSON platform.
When things don’t line up
Molecular modelers frequently encounter misaligned fragments coming from different file sources, modeling sessions, or conformer libraries. When atomic structures come loaded with arbitrary coordinates, operations like docking, visualization, or energy calculations can become difficult. The classic manual translation of each fragment tends to be slow and imprecise — not to mention error-prone.
SAMSON’s solution allows you to quickly reposition and orient molecular structures using intuitive menus and widgets, reducing manual effort and providing geometric precision.
Fast alignment via context menu
Want to center a molecule at the origin or align it with an axis? Here’s how:
- Right-click a molecular structure (or on the selection in the Document view).
- Navigate to Move selection.
- Choose your desired operation: Center on the origin, Align with X axis, Align with XY plane, and more.
This quick method saves time during the model preparation phase and is helpful when building symmetrical systems.
Align and distribute via Edit Menu
For larger jobs — such as distributing multiple molecules or lights evenly in space — head to:
- Edit > Align for aligning multiple objects with shared axes or orientations.
- Edit > Distribute to space elements evenly.
These commands are useful when assembling periodic structures or visualizing molecular arrays.
Work directly with the compass
If you prefer to work visually, simply right-click on any axis of the compass widget displayed in the viewport. You’ll be given context-aware alignment options (e.g., align to X axis, center along Z plane, etc.).
Snapping makes it smoother
Enabling the grid overlay at the bottom of your viewport is a great way to visualize planes and promote consistent placement. Toggle snapping options in the top-left corner of the viewport or via Interface > Preferences > Editors > Snapping. Snapping can apply to both translation and rotation, allowing you to align fragments with sub-angstrom and degree precision.
Conclusion
Whether you’re preparing publication figures or building molecular containers, SAMSON’s alignment features provide intuitive geometric control for molecular structures, lights, and meshes. By learning how to efficiently center, align, and distribute your systems, you’ll spend less time wrangling coordinates and more time exploring your models.
To learn more and explore additional options such as scripting and move editors, visit the full documentation page: 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.