When working with complex molecular models, precise alignment becomes critical—especially when comparing structures, preparing input files for simulations, or creating meaningful visualizations. Misaligned structures can lead to errors in analysis, inefficient setups for simulations, and ambiguous visual outputs. Fortunately, SAMSON provides helpful tools that allow you to quickly and accurately align molecular structures with respect to global axes or planes.
This post introduces how to use SAMSON’s built-in alignment features to reposition molecules using global frames of reference. This avoids guesswork and ensures your models are presented and analyzed in a consistent, reproducible orientation.
Why structure alignment matters
Imagine aligning a ligand with a receptor, orienting simulation boxes, or placing building blocks in a crystal structure. Small discrepancies in orientation can become large-scale problems when analyzing symmetry or measuring changes, such as rotation or translation, between conformations. Aligning structures before applying further operations reduces human error and ensures repeatable scientific workflows.
How to align molecular structures in SAMSON
In SAMSON, you can align selected atomic structures with respect to the global frame (XYZ axes or planes such as XY, YZ, or XZ) using just a few clicks.
- Right-click on any structure in the viewport or Document View to bring up the context menu.
- Navigate to Move Selection.
- Choose one of the alignment options:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, XZ, or YZ plane
There’s no need to manually toggle any tools: the action is applied immediately to the selected nodes. For best results, ensure that your selection includes structural nodes with atoms (rather than higher-level representations or files).
Visualize alignment with the grid
To assist with alignment, you can toggle the grid display in SAMSON’s viewport. The grid represents the XY plane at Z = 0 of the global coordinate system. This helps you see how structures are oriented with respect to the origin.
To activate the grid, look for the grid toggle in the bottom menu of the viewport. This simple visual guide can provide affirmation that your alignment operation completed successfully.
Tip
You can make combined use of Align and Distribute options (found in Edit > Align) for batch modifications of assemblies or placing molecules evenly in space.
Faster workflows with reliable reference frames
The more models you handle, the more important automated alignment becomes. Whether you’re preparing figures or aligning fragments for docking runs, aligning structures with respect to the global reference frame reduces repetitive manual manipulations.
To explore other movement options, such as translating or rotating structures using widgets or move editors, check out the full documentation below.
Learn more in the SAMSON Documentation.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.