When you’re building molecular structures from scratch, particularly for custom molecules or intermediates, the process often starts with adding atoms one by one. In SAMSON, there are two primary ways to do this — and both offer distinct benefits depending on your modeling needs.
But if you’re wondering whether you should substitute an atom or create a new bond, you’re not alone. This is one of those underrated parts of molecular modeling where getting it right makes the difference between a structurally clean result and a confusing tangle of atoms.
Option 1: Substitution Mode
Use case: Replace a hydrogen with another atom or fragment, while maintaining molecular geometry and valence accuracy.
To perform a substitution in SAMSON:
- Hover above the atom you want to substitute (typically hydrogen).
- Click to place the new atom in its place.
This method is particularly elegant when you want SAMSON to automatically adjust bond lengths and orientations based on atomic radii. For example, substituting a hydrogen in methane with a carbon automatically rebalances bonds in the resulting ethane-like structure.
Visually, SAMSON helps by providing green overlays when a substitution is valid, and red overlays when it’s not.
Option 2: Bonding Mode
Use case: Connecting two atoms with a new bond in a flexible manner, such as building chains or frameworks manually.
To add a bond instead:
- Click and hold on an atom in the viewport.
- Drag your mouse to set a bond distance, then release to place the atom.
This allows more control over atom placement, especially in complex geometries or when the structure doesn’t follow standard hybridization geometries.
The automatic hydrogen adjustment feature (enabled by default under Preferences > Editors > Add) ensures that newly added atoms integrate correctly into the molecular structure.
So, which should you use?
If your workflow involves assembling known fragments like functional groups or residues where valence and geometry really matter, use substitution. It keeps structures clean and chemically sound.
If you’re laying down an initial configuration or exploring arrangements, bond-based addition gives more spatial flexibility.
Combining both methods speeds up buildup while maintaining control over molecular geometry.
And don’t forget that you can activate Interactive Minimization — press Z — to live-optimize geometry as you build. Watching your molecules stabilize in real-time is always satisfying.
To learn more about building atoms and other molecular editing techniques, check the full documentation: 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