Precise manipulation of molecular structures is a core task in molecular modeling. Whether you’re preparing models for simulations, visualizations, or comparative studies, structural alignment plays a vital role. Yet, aligning molecules accurately in 3D space can be time-consuming if the right tools are not readily accessible.
In SAMSON, the integrative molecular design platform, structure alignment tools are built directly into the editing interface so you can quickly and precisely align molecules or fragments along axes or planes of the global coordinate system. In this post, we’ll walk through how to do this using the context menu and compass widgets. You’ll also learn how to combine these with the grid display for enhanced spatial orientation.
When Do You Need Alignment?
Here are a few common scenarios where alignment features can save time and increase accuracy:
- Overlaying molecules for structural comparison
- Setting up systems for crystallography-related tasks
- Generating clean, standardized inputs for simulations
- Placing fragments in ideal orientations for linking or bonding
Aligning With the Global Reference Frame
The global frame in SAMSON consists of the classic X, Y, Z axes and XY, YZ, XZ planes. You can align any atomic structure, mesh, or light directly with any of these using a simple right-click approach:
- Select your structure or group of atoms.
- Right-click on the selection (either in the viewport or in the Document view).
- In the context menu, hover over Move selection.
- Choose the desired alignment option:
- Center on the origin
- Align with X/Y/Z axis
- Align with XY/XZ/YZ plane
Tip: Activate the Grid for Reference
To better visualize how the structure aligns with the global reference frame, switch on the grid from the bottom menu of the viewport. This grid shows the XY plane at Z=0.
This visual reference can be extremely helpful, especially when using snapping or needing to orient multiple molecules in regular arrays.
Align via Compass Widgets
SAMSON also features interactive compass widgets – small, draggable orientation tools that sit in the corner of the viewport. Right-clicking on these brings up alignment options related to the compass direction:
This method is especially convenient if you’re visually assessing spatial orientation and prefer fewer menu clicks.
Batch Align and Distribute
Multiple structures can also be arranged using the Edit > Align and Edit > Distribute commands. This is useful when laying out a series of molecules or meshes with uniform spacing or orientation.
This functionality accelerates model building and is especially useful in molecular docking setups, building supermolecular assemblies, or preparing visual diagrams for papers and presentations.
Bring More Order to Your Molecular Workspace ✨
By mastering these alignment tools, you remove ambiguity from your modeling process and reduce time spent repositioning molecules manually. These techniques also improve the visual clarity and credibility of your structural work.
To learn more about manipulating molecular objects in SAMSON, including translations, rotation, snapping, and pivot control, visit the full documentation page at https://documentation.samson-connect.net/users/latest/moving-objects/.
SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.