Building molecules atom by atom is a powerful and precise method, but for many molecular modelers, it can also be time-consuming when dealing with larger or repetitive structures. If you ever felt that constructing molecules takes too long or involves too many repetitive steps, working with fragments in SAMSON might be the practical solution you’re missing.
SAMSON allows you to build complex molecular systems by assembling pre-defined or user-defined molecular fragments instead of adding every atom manually. This is especially helpful when modeling molecules like bisphenols, saccharides, peptides, or any structure built from recurring units.
What Are Fragments?
Fragments can be atoms, functional groups, rings, radicals, or full molecules. These are accessible from the Asset Browser in SAMSON. Using these reusable building blocks can significantly reduce modeling time while increasing accuracy.
Getting Started with Fragment-Based Building
To build molecules from fragments:
- Open the Asset Browser from the interface.
- Select a predefined fragment, such as phenol from the Aromatics folder.
- Activate the Add editor and double-click on the fragment to bring it into the viewport.
- Click in the viewport to place the fragment and start assembling your molecule.
If you’d like to change which atom in the fragment is used for substitutions, simply press and hold the Ctrl (or Command on macOS) key and click on the desired atom within the fragment. Green overlays indicate valid connections, while red ones help you avoid implausible structures (this behavior can be adjusted in Preferences).
Combining Fragments: An Example with Bisphenol A
To illustrate the workflow, here’s how to build Bisphenol A (BPA) using fragment assembly:
- Start by building a propane core (C3H8) from carbon atoms.
- Switch to using the phenol fragment.
- Change the substitution atom to the aromatic carbon of your choice.
- Substitute two hydrogen atoms on the central carbon of propane with phenol fragments.
- Enable interactive minimization (Z) to relax the structure as you build.
This approach leads to faster molecule assembly and easier handling of symmetrical structures or repeated motifs.
Working with Custom Fragments
You’re not limited to predefined fragments — you can use any part of a molecule as a fragment:
- Select part of your molecule using the Select editor.
- Right-click on the selection and choose Use selection to build.
- The selected part will now behave like a fragment, ready for insertion elsewhere.
It’s also possible to rotate and move fragments precisely using SAMSON’s Move editors. You can rotate fragments into position while they are highlighted or selected, and apply further refinement using interactive minimization.
Why Use Fragments?
Fragment-based modeling streamlines your workflow:
- Reduce manual input (especially helpful for large structures)
- Maintain consistency in recurring units
- Experiment with molecular replacements more rapidly
Whether you’re building organics, nanomaterials, or drug candidates, using fragments in SAMSON can help you set up molecular systems faster and with fewer errors.
🎯 Tip: Always check and configure your fragment placement preferences in Preferences > Editors > Add to adjust behaviors like hydrogen adjustment, overlap prevention, and fragment orientation.
To learn more about building with fragments in SAMSON, visit the full documentation page: https://documentation.samson-connect.net/users/latest/building-molecules/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.