If you work with molecular models, chances are you’ve run into the frustration of misaligned structures. Whether you are comparing different conformers, preparing models for visualization, or setting up simulations, having your molecules neatly organized in the coordinate space is critical.
Often, users resort to manually adjusting positions—an approach that’s time-consuming, error-prone, and hard to reproduce. If you’ve ever wished for a more reliable and efficient way to quickly organize your molecular scenes, the solution may already be in your toolkit: SAMSON’s alignment tools.
Why alignment matters
Molecular modeling isn’t just about building molecules—it’s also about positioning them for interpretation, analysis, or simulation. For example, aligning ligands to a receptor, comparing alternative binding poses, or preparing data for machine learning models all require consistent positioning across structures.
SAMSON offers built-in tools to align atomic structures, meshes, and even lights in the global reference frame (X, Y, Z axes). These tools help you consistently organize your data, and they’re only a couple of clicks away.
Using the context menu for alignment
To quickly align a structure with respect to a global axis or plane:
- Right-click the structure you want to align (or use the selection in the Document view).
- Navigate to Move selection in the context menu.
- Select from options like Center on the origin, Align with X axis, Align with XY plane, and others.
Visual cues: enabling the grid
When aligning objects to planes (like XY or XZ), it helps to visualize the spatial orientation. You can toggle the grid in the bottom menu of the viewport to see the XY plane at Z = 0. Instant feedback helps ensure the alignment meets your expectations.
Distribute and organize with precision
If you’re dealing with multiple objects, SAMSON also includes commands under Edit > Align and Edit > Distribute. These are especially useful for arranging repeated subunits or optimizing layouts in workshops, presentations, or publications.
Try the compass widget
Still looking for a faster workflow? Right-click on a compass widget in the viewport for alignment commands that orient structures in a single click.
Conclusion
If aligning your molecular data has ever felt clunky, SAMSON’s set of alignment tools can streamline this crucial step in your workflow, making molecular modeling faster and more reproducible.
Explore SAMSON’s alignment tools in more detail in the original documentation: Moving Objects in SAMSON
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON here.