Editing

Placing and Replacing Atoms

With an element selected from the periodic table:

Click an existing atom

Replaces that atom's element with the currently selected element. Use this to substitute atoms in a structure — for example, turning a carbon into a nitrogen.

Click empty space

Places a new atom at the click position. If existing atoms are nearby, a bond is created automatically. Use this to start a new fragment or extend a chain.

Selecting Atoms

• Click an atom to select it.
• Hold Shift and click to add more atoms to the selection.
• Click empty space to clear the selection.

The active selection drives the geometry editor and delete operations.

Adjusting Geometry

Select 2, 3, or 4 atoms to expose the matching geometry control:

Selection	Control	What it does
2 atoms	Bond distance	Stretch or compress the bond
3 atoms	Bond angle	Open or close the angle
4 atoms	Dihedral angle	Rotate around the central bond

Changes apply immediately and update the viewport.

Toolbar Actions

Action	What it does
Undo	Reverts the last editing step
Delete	Removes selected atoms and their bonds
Optimize	Relaxes the full structure

Clear resets the entire canvas and removes all atoms. It asks for confirmation before proceeding. Use this when you want to start over from scratch.

Tips

• Relax early. After adding a few atoms, click Optimize to avoid large distortions before continuing.
• Use fragments for speed. The fragment library inserts ring systems and common groups faster than atom-by-atom placement. You can also type a custom SMILES string to insert any fragment.
• Check torsions before running. After any large edit, check dihedral angles — especially around rotatable bonds — before switching to Run Mode.