Aligning molecular structures in 3D space is a common task in molecular modeling workflows. Whether you’re preparing a system for analysis, visualizing structures together, or setting up simulations, the ability to quickly and accurately align molecules along reference axes or planes can save time and improve reproducibility.
This blog post provides a step-by-step guide to aligning structures visually using SAMSON’s built-in tools—without having to write any Python scripts. Everything takes place through an intuitive graphical interface based on context menus and simple commands.
Why Molecular Alignment Matters
Precise positioning of molecules is crucial in many situations:
- You need to compare fragments of different molecules in a consistent orientation.
- You are preparing a structure for docking or dynamics simulation.
- You want to align parts of a macromolecular assembly.
- You want better clarity or symmetry in your visualization.
Instead of relying on external programs or alignment scripts, SAMSON offers built-in tools to get this done directly in the viewport.
Aligning Structures in the Global Frame
SAMSON uses a global reference XYZ frame that enables consistent placement of structures. You can align any selected structure to key orientations within this frame using the context menu:
- Right-click a structure in the Document view or right-click the current selection in the viewport.
- Navigate to Move selection in the context menu.
- Select from the following alignment options:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, XZ, or YZ plane
This is an effective way to bring all structures into a common orientation for precise comparison or further editing.
Tip
To visualize alignment better, enable the grid in the bottom menu of the viewport. This grid corresponds to the global XY plane at Z=0.
Distribute and Align Groups of Objects
SAMSON also lets you align or distribute multiple objects at once, including molecules, meshes, or lights:
- Use Edit > Align to bring multiple objects into alignment along common axes or planes.
- Use Edit > Distribute to space out objects evenly.
You can also access similar alignment options directly from the compass widgets in the viewport. Right-click on a compass element to align structures intuitively.
When to Use This Approach
This method is ideal if:
- You prefer graphical tools over scripting.
- You frequently reposition or compare model components.
- You want a quick quality-of-life improvement that enhances modeling efficiency.
Want to Learn More?
The documentation has full details and more examples of structure control in SAMSON: Moving Objects Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.