Assembling a molecule from fragments can feel deceptively simple: choose a piece, place it, and connect it. In practice, the difficult part is often knowing whether the connection is sensible, which atom should attach, and how to recover when a fragment lands in an awkward orientation. A small number of deliberate setup choices can make the process easier to inspect and refine.
This workflow uses SAMSON’s Add editor to assemble fragments while keeping an eye on substitution, orientation, and hydrogen adjustment. The visual cues are useful guidance, but they are not a substitute for checking the chemistry and geometry of the structure you intend to model.
Set up before placing fragments
Open Preferences > Editors > Add and review the options before you begin. For a typical fragment-building workflow, consider enabling Adjust hydrogens when adding fragments, Automatically orient fragments on substitution, Merge neighboring atoms, and Prevent unexpected substitutions. These settings help SAMSON adjust hydrogens, position a fragment during substitution, merge nearby atoms when appropriate, and flag operations it considers implausible.
The green and red overlays are especially useful as a pause point: green indicates an operation the builder considers acceptable, while red indicates one it considers forbidden under the current settings. Treat these as cues to inspect the proposed connection, not as a guarantee that the resulting structure is scientifically correct. If you deliberately need to override a recommendation, the preference controlling unexpected substitutions can be changed.
Choose the connection method deliberately
With the Add editor active, select an atom or asset in the Asset Browser. The browser includes default fragments and can also provide access to assets obtained through SAMSON Connect. Use Filter assets… to find a fragment, and double-click an asset to make it the current building fragment.
There are two useful ways to attach a new piece:
- Substitution: hover over the atom to replace and click. The new fragment is positioned with the substitution atom taking the place of the clicked atom. This is useful when replacing a hydrogen or another leaving position with a group.
- Bond creation: press and hold on the atom you want to connect to, move the cursor away to a bond-like distance, and release. This is useful when adding a fragment through a new connection rather than replacing an existing atom.
Before committing a substitution, confirm that the intended atom in the fragment is the one being used. Hold Shift while building to choose the fragment atom and bond used for substitution. For a fragment you created from a selection, use Ctrl on Windows or Linux, or Cmd on macOS, to choose a different substitution atom. This is a small step that can prevent a correctly oriented fragment from attaching at the wrong site.
Use a small test build to learn the controls
If you are new to the editor, try a simple structure before working on a larger molecule. Add a carbon atom from the Asset Browser, then connect another carbon by substitution or by creating a bond. With hydrogen adjustment enabled, SAMSON adds hydrogens based on valences as best as possible. Continue with other atoms if needed, and use the Periodic Table for atom types that are not available among the quick-access choices.
Keep an eye on the viewport’s snapping controls. Translational and angular snapping can affect where fragments are placed. Snapping is helpful when you want regular spacing; if you are following a free-form tutorial, setting both options to Off avoids introducing an unintended grid or angle constraint.
Orient, then relax
Automatic orientation can help place a fragment without overlapping nearby atoms, but you may still want to adjust it yourself. Newly added fragments are selected automatically; otherwise, select the part you want to move. Press M to activate the Local Move Editor. To change the rotation pivot, zoom in enough to see the atom clearly, then click that atom. Rotate with the controller’s trackball or its axis controls. To rotate around a bond, click the bond with the Local Move Editor active.
Interactive minimization can be switched on or off with Z (or through Edit > Minimize). It can relax geometry during construction or after you have assembled the pieces. Minimization is a geometry-relaxation step, not a replacement for checking connectivity, bond orders, formal charges, or the intended chemistry.
Make corrections without losing your place
If a bond order needs changing, activate the Edit bonds editor with B, hover over the bond, and use + or –. To change an atom’s formal charge, activate Edit charges with C and use the corresponding controls over the atom. Note that changing bond order through the Inspector does not automatically adjust hydrogens. Undo and redo are available from Edit > Undo and Edit > Redo, so you can test a placement and back out if it is not what you intended.
A reliable habit is to check the result after each connection: confirm the attachment atom, inspect the overlay, look for overlaps, and verify bond order and charge when relevant. For more on building with atoms and fragments, orienting structures, and editing the document hierarchy, see the SAMSON Building molecules documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.