When working on multi-component molecular systems—such as protein-ligand complexes, nanostructures, or assembling ligand libraries—being able to precisely align and position structures is essential. But manual alignment can be both time-consuming and error-prone, especially when scaling operations or ensuring consistency across different reference frames.
In SAMSON, aligning molecular structures is both quick and intuitive, thanks to a set of built-in tools that integrate cleanly into the software’s viewport and interface. Whether you’re centering a molecule on the origin or distributing multiple structures along an axis, these built-in actions can drastically increase your efficiency 🧪.
Why Structure Alignment Matters
If structures are not properly aligned, simulations can give inaccurate results, visualizations can be misleading, and reproducibility becomes harder to achieve. For example, if you’re creating a symmetrical molecular assembly or setting up a docking experiment, misaligned geometries can spoil the setup.
How to Align Structures in SAMSON
SAMSON offers several ways to align structures:
- Center molecules on the origin
- Align structures along X, Y, or Z axes
- Align to XY, XZ, or YZ planes
All these options are available directly from the context menu:
- Right-click on the structure (or selection) you want to align.
- Go to Move selection in the menu.
- Choose your preferred alignment:
- Center on the origin
- Align with X axis, Y axis, or Z axis
- Align with XY, XZ, or YZ plane
Need to Align or Distribute Multiple Structures?
SAMSON also makes it easy to align or distribute multiple entities across your workspace. This is especially useful when working with repeated units or setting up arrays of molecules or meshes.
Go to Edit > Align or Edit > Distribute in the main menu to find commands such as:
- Align left, center, or right
- Distribute evenly along an axis
Tip: Use the Compass for Quick Access
You can also align structures using the Compass. This widget appears in the viewport and allows you to align quickly using its context menu. Right-click the compass to access alignment shortcuts related to global axes and planes.
See It In Action
If you’re more of a visual learner, this short video demonstrates how to align and distribute structures using the built-in tools:
Final Thoughts
Whether you’re working on large molecular assemblies or simply want to position ligands for docking, SAMSON’s alignment tools can help you save time and reduce manual adjustments. And because those features are deeply integrated into the platform’s standard menus and interface elements, they’re always just a click—or right-click—away.
To learn more about structure alignment and movement in SAMSON, please visit the full documentation: Moving Objects Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON here.