Repositioning molecules is one of those routine tasks that can quickly become a bottleneck in molecular modeling workflows. Whether you’re preparing a simulation system, organizing figures for a presentation, or simply exploring molecular interactions, aligning structures precisely and efficiently is often harder than it should be—especially when dealing with complex multi-component assemblies.
If you’ve ever tried to align fragments with respect to a global frame or distribute molecular units into an ordered layout, you may have faced awkward pivot points, unresponsive interfaces, and countless undos. Fortunately, SAMSON, the integrative molecular design platform, offers an intuitive and flexible way to perform these alignments—visually and interactively—in just a few clicks.
Align Structures with Context Menus
One of the fastest methods to align a structure in SAMSON is to use the context menu. Right-click on any selected molecule or structure—or click on a selected group in the Document View—and navigate to:
Move selection > [Alignment Option]
You can choose from options such as:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, XZ, or YZ plane
This works well for quickly orienting molecular units around specific spatial axes, for example if you’re preparing them for comparative visualization or simulation input.
Use the Viewport Grid for Visual Reference
If visual orientation is important, you can switch on the grid in the bottom menu of the Viewport. This displays the global XY plane at Z=0, providing a helpful 3D reference when aligning components.
Align and Distribute Multiple Structures
For more advanced layout operations, go to:
Edit > Align or Edit > Distribute
You can align or distribute not just atoms, but also lights and meshes. This is especially useful when creating presentation-ready compositions or setting up evenly spaced systems like molecular arrays.
For example, using these features you can:
- Space out repeated structures evenly in one or more directions
- Align molecular axes so that their reference atoms line up
- Consistently orient fragments to compare their shapes or properties
Align from Anywhere Using the Compass
You can also right-click on the Compass widget (located in the Viewport) to access alignment options that make use of the global XYZ axes. It’s a convenient way to access the same orientation options without needing to navigate through menus.
Conclusion
Being able to align atomic structures quickly—without leaving the visual environment—makes modeling faster and less error-prone. SAMSON combines visual tools and precise snapping to help users get alignment right the first time, making modeling more intuitive for both new and experienced users.
To learn more 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 get SAMSON at https://www.samson-connect.net.