When constructing molecular systems, a frequent challenge faced by researchers is correctly orienting molecular fragments before and after placement. Improper orientations can lead to overlapping atoms, energetically unfavorable structures, and ultimately incorrect simulation results downstream.
SAMSON provides several integrated tools that make fragment orientation and alignment both intuitive and precise. In this post, we explore how to effectively control fragment orientation when building molecules using SAMSON.
Why orientation matters
Whether you’re attaching a single phenol ring or constructing entire functional groups, fragment orientation directly affects molecular geometry. For instance, connecting a fragment without properly aligning the reactive site can result in poor angles, bond lengths, or even steric clashes. Manual manipulations can be tedious and error-prone—unless you use the right tools.
Automatic orientation during fragment substitution
When using the Add editor in SAMSON, fragments are automatically oriented to their target atoms, thanks to intelligent prediction features. Green and red overlays appear to indicate acceptable and forbidden connections, helping users avoid substitution errors.
Manual orientation control using Move Editors
If needed, you can manually adjust orientations using Move Editors:
- Local Move Editor (M) allows rotation and translation of the selected fragment relative to a pivot point.
- Global Move Editor (K) rotates and moves fragments with respect to the entire structure.
- Clicking on a bond with the Local Move Editor will enable rotation around that bond only.
Here’s an example of how to rotate a fragment around a bond axis to find the most suitable alignment:
Set your pivot wisely
In the Local Move Editor, you can set a custom pivot atom by simply clicking the desired atom after selecting the fragment. This means you can rotate around any point in your fragment—not just geometric centers.
Snapping: alignment made easier
To aid in placing fragments at precise distances and angles, SAMSON offers snapping options (translational and angular) accessible in the top-left corner of the viewport. These options are especially useful for symmetrical assemblies or aligning fragments on a grid.
A quick tip
You can rotate the fragment before placing it by holding Shift + right-click. This allows you to visually preview and set the correct alignment before committing to the addition.
For those building large molecular structures—such as supramolecular assemblies or functionalized surfaces—mastering these orientation tools can save time and significantly improve your workflow.
To learn more, visit the full documentation page on building molecules with SAMSON.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can download SAMSON at https://www.samson-connect.net.