One common challenge in molecular modeling is aligning molecular fragments precisely — especially when assembling large systems. Misoriented fragments can lead to structural clashes and inaccurate simulations. If you’ve ever found yourself frustrated by overlapping atoms or spent too much time rotating fragments manually, this post is for you.
In this guide, we focus specifically on how to orient molecular fragments in SAMSON, a powerful platform for molecular design. SAMSON includes several tools that make it easier to control fragment orientation without scripting or complicated workflow setups.
Rotating a Fragment Around a Specific Atom 🔄
When modifying a molecule or adding a functional group to an existing structure, clean positioning matters. SAMSON provides a Local Move Editor (shortcut: M), which allows you to rotate selected fragments with precision.
To orient a fragment:
- Select the fragment you just added (it’s often selected automatically).
- Press M to activate the Local Move Editor.
- Click on the atom you want to use as the pivot. This sets your rotation center.
- Use the on-screen rotation controls (trackball or arrows) to rotate the fragment with accuracy.
This is especially helpful when, for example, fine-tuning the position of a sugar moiety or minimizing steric hinderance between a ligand and binding pocket.
Rotating Around Bonds
Sometimes you want to rotate a single part of a molecule around a bond to explore conformations, such as in rotamer analysis or side-chain adjustments. It’s possible to do this with just one click.
Here’s how:
- Activate the Local Move Editor (shortcut: M).
- Click on the bond you want to rotate around.
- SAMSON will automatically detect the smaller fragment and attach move controls.
You can apply manual rotation using the handles or reposition the fragment as needed. Here’s how that works in practice:
Snapping and Precision Placement
SAMSON also includes snapping tools for better control:
- Translational Snapping: Enforces specific distances between placed atoms/fragments.
- Angular Snapping: Helps align angles precisely during rotation.
You’ll find these settings in the top-left corner of the viewport once you’re in Add mode. If you want total manual control, you can disable snapping anytime.
Aligning Multiple Copies: A Case for Reproducibility
If you’re duplicating structures—say, building symmetric multimers or nanoparticle surfaces—the Global Move Editor (shortcut: K) offers ways to control rotation and pivoting of entire molecules around a specified center. Here’s a video illustrating how to do that step-by-step:
More Moving Options
Need more? SAMSON includes multiple movement editors, accessible from the menu on the left-hand side of the viewport. Each one offers slightly different behavior suited to local, global, or constrained motion.
Ready to stop guessing fragment orientation and start placing things exactly as you want?
Head over to the original SAMSON documentation page to learn more.
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.