Aligning molecular structures can be a repetitive task in molecular modeling, especially when working with multiple structures or preparing publications and interactive presentations. Minor misalignments can have a noticeable impact on how data is interpreted. But if you’re using SAMSON, there’s a simple, precise way to align atoms, meshes, and other visual components — one that often goes unnoticed.
Why structure alignment matters
Whether you’re comparing conformers, assembling a large supramolecular system, or just trying to make snapshots more visually appealing and interpretable, tidy alignment saves time and improves clarity. SAMSON provides tools that align and distribute components using a global reference frame — with minimal effort and without scripting.
Aligning with the global reference frame
You can align atoms, groups, or entire molecular structures along global XYZ axes or planes. This is very useful to assess structural symmetry, or to prep structures before simulations or publications.
Here’s how to do it:
- Right-click on a structure or on a current selection in the Document view.
- In the context menu, choose Move selection, and then pick the alignment of your choice.
The options include:
- Center on the origin
- Align with X, Y, or Z axis
- Align with XY, XZ, or YZ plane
This isolates the structural component to a known orientation or location in space. Here’s a visual example of this process from the documentation:
Combining alignment and distribution
Once aligned, you may also want to distribute your objects evenly, e.g., for creating symmetric arrangements or comparison panels. SAMSON has dedicated commands for this in Edit > Align and Edit > Distribute.
Using the Compass
For even faster access, try using the Compass widget directly in the viewport. Right-clicking on it opens up alignment commands — a useful shortcut when you’re navigating and adjusting your scene interactively.
Tips for better alignment:
- Switch on the grid in the viewport menu to see the XY plane at Z=0. This gives you a clear visual frame of reference.
- Combine snapping options with alignment to prevent slight drifts or inconsistent positioning.
- Use undo (Edit > Undo) anytime to reverse an unintended adjustment.
These tools are particularly valuable when building large scenes, creating animations, or preparing publication-ready figures.
For a hands-on demonstration, SAMSON’s documentation offers a step-by-step guide.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.