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Molkit

Atom Numbering

Atom numbers are small labels drawn next to atoms, useful for naming exercises, NMR assignments, and referring to specific positions in a structure. Numbers are stored on each atom, so they survive saving, copying, and moving atoms. All numbering commands live in the Structure menu under Atom Numbering.

Automatic numbering

Choose Structure, then Atom Numbering, then Auto-Number Atoms.

  • With no selection, every atom is numbered. Each connected fragment is traversed breadth-first starting from a terminal atom (one with a single bond), so numbers run sequentially along chains. Separate fragments continue the count rather than restarting at 1.
  • With atoms selected, only those atoms are numbered, in the order you selected them (1, 2, 3, and so on).

Auto-numbering turns number visibility on if it was off.

Manual numbering

To set or edit a single atom’s number:

  • Select the atom and type a value in the Number field of the Numbering section in the Object Properties panel. Click the X button next to the field to clear it.
  • Or right-click the atom and choose Set Atom Number. Leave the prompt blank to clear the number.

With several atoms selected, right-click and choose Number N Atoms (1, 2, 3…) to number them sequentially in selection order.

To remove numbers, choose Structure, then Atom Numbering, then Clear Atom Numbers. This clears the selected atoms, or every atom if nothing is selected.

Visibility

Structure, then Atom Numbering, then Show Atom Numbers toggles all numbers on or off without deleting them. Numbers are kept on the atoms and reappear when you toggle visibility back on.

Appearance and position

Numbers default to a small blue label placed automatically around the atom. To change the global color, size, or font, choose Structure, then Atom Numbering, then Number Style.

Once an atom has a number, the Numbering section in the Object Properties panel also offers per-atom overrides: position (Top, Left, Bottom-Right, and so on), color, size, and font. You can also drag a number label directly with the Select tool to place it anywhere; alignment guides snap it relative to the atom label.

Renumbering after edits

Numbers do not update on their own when you add or delete atoms. After changing a structure, run Auto-Number Atoms again to get a clean sequence.

See also