A fragment can look perfectly reasonable on its own and still be awkward to connect to a growing molecule. It may overlap nearby atoms, attach through the wrong site, or leave hydrogens that no longer fit the intended structure. These small problems can interrupt a modeling workflow—and make it harder to tell whether the structure or just the placement needs attention.
SAMSON’s Add editor helps manage these decisions while you build. The key is to treat fragment assembly as a sequence: choose the attachment point, preview the proposed connection, then check the resulting geometry and structure.
Start with the right building block
Use the Asset Browser to find a ready-made fragment, or turn a selection in your document into a building fragment. The Asset Browser includes folders of assets and a filter for searching them. Double-clicking an asset activates it as the current fragment in the Add editor.
When using a fragment you constructed yourself, select it in the Document view or Viewport, right-click, and choose Use selection to build. If the default substitution atom is not the one you need, hold Ctrl on Windows/Linux or Cmd on macOS and choose the desired atom in the fragment.
Choose how the connection should happen
There are two useful ways to attach atoms or fragments. Substitution replaces an atom in the existing structure: hover over the atom to replace and click. This is useful when a hydrogen or other leaving site marks where the new group belongs. The Add editor takes covalent radii into account when positioning the new fragment.
Bond creation connects the new fragment to an existing atom without using the same replacement action. Press and hold on the atom you want to connect to, move the pointer away to a bond-like distance, then release. If the placement or connection is not what you intended, undo is available through Edit > Undo.
Read the preview before committing
When the relevant preference is enabled, SAMSON shows acceptable operations with a green overlay and forbidden ones with a red overlay. Treat this as a useful check before clicking: a red preview is a prompt to reconsider the attachment site or the proposed substitution. The Prevent unexpected substitutions preference controls whether these recommendations are enforced or can be overridden.
Fragment orientation can also be predicted automatically when connecting to an existing molecule. This helps position the added atoms away from overlaps as far as possible. If the automatic orientation is not the one you want, you can rotate the fragment manually: hold Shift and right-click to rotate while building, or use a Move editor after adding it.
Let hydrogens and geometry catch up
Before assembly, check Preferences > Editors > Add. With Adjust hydrogens when adding fragments… enabled, SAMSON adjusts hydrogens as best as possible when adding or linking atoms and fragments, changing bond order, or changing formal charge. The Merge neighboring atoms option can merge nearby atoms when a fragment is connected, while Create new structural models when adding non-covalent fragments controls whether separate non-covalent additions receive their own structural model.
For an additional geometry check, interactive minimization can run while you build. Press Z to switch it on and press Z again to stop. This is especially helpful after a connection, but it does not replace checking that the intended atoms and bonds are present.
A practical order is: select the fragment, confirm its substitution atom, inspect the preview, make the connection, then review the result and minimize if needed. If the fragment is correct but its position is not, use a Move editor to orient it. For more guidance, see the SAMSON Building molecules documentation.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Get SAMSON.