When building or modifying molecular models, structure alignment may seem like a small step—but it can have a big impact. Misaligned atoms or molecules can lead to misleading visuals, unnecessary complexity during simulation, or trouble when exporting for publications or sharing with collaborators. For this reason, SAMSON includes several alignment tools that can make your molecular workspace neater and more productive.
This article outlines how to quickly align atomic structures, meshes, or lights in SAMSON using the global reference frame or distribution tools.
Why Align Structures?
In molecular modeling projects, especially those involving multiple fragments or assemblies, consistent structure orientation is key:
- Easy to analyze and compare conformations
- Helps layout symmetric arrangements of molecules
- Improves visualization and presentation clarity
- Prepares input for simulations or docking procedures requiring well-defined positions
Aligning in the Global Reference Frame
The global reference frame in SAMSON is based on traditional X, Y, Z Cartesian coordinates. You can align molecules along these axes or their associated planes.
To perform an alignment:
- Right-click on an atomic structure in the viewport or Document view
- Navigate to Move selection in the context menu
- Select one of the available alignment options, such as:
- Center on the origin
- Align with X/Y/Z axis
- Align with XY/XZ/YZ plane
Tip: Turn on the grid in the bottom menu of the viewport to see where the XY plane (Z=0) lies.
Align and Distribute Multiple Structures
Once your molecule is aligned, you may want to replicate it or spread multiple copies evenly. SAMSON supports this through its Edit > Align and Edit > Distribute commands.
These tools are useful for:
- Creating arrays of molecules, such as nanotube segments or crystal-like patterns
- Spacing mesh or light objects equally in visualization scenes
Bonus: Use the Compass
Right-clicking on the compass widget in the viewport allows quick access to alignment commands. This offers a more intuitive and interactive way to align components without menus.
Wrapping Up
Properly aligning molecular structures helps avoid preventable confusion and saves time during simulations or presentations. Whether you’re positioning a receptor for docking studies, comparing conformers, or building nanostructures, structure alignment in SAMSON is a fundamental step with significant benefits.
To learn more about structure alignment and object movement in SAMSON, visit the full documentation here: https://documentation.samson-connect.net/users/latest/moving-objects/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.