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Molkit

Atom Tool

Molkit has no separate atom tool. Atom placement and element changes are part of the Bond tool (B): click empty canvas to place a lone atom of the active element, click an existing atom to change its element, and drag from an atom to grow the structure. This page covers choosing elements and editing atom labels.

The element picker

The picker column on the right edge of the canvas sets the active element. It holds the common elements C, N, O, H, S, P, F, Cl, Br, I, plus R (generic substituent) and X (generic leaving group), which are placed as labels on a carbon. The grid button at the bottom of the element row opens a full periodic table popup; click any cell to make that element active.

Below a separator, the same column carries functional group buttons (OH, NH2, CH3, COOH, NO2, CN) and abbreviation buttons (Me, Et, Ph, OMe, tBu, Ac), each with a “More” browser. The Abc/Str toggle controls whether a group is placed as a label or as a drawn structure. See Abbreviations.

Element shortcuts

Single keys set the active element: C, N, O, S, P, F, I. Two are conditional: P opens the Properties panel instead when atoms or bonds are selected, and F flips the bow of a selected curved arrow first. There are no shortcuts for H, Cl, or Br (H and B are taken by other tools).

Changing an existing atom

Three ways:

  • Bond tool click. With the Bond tool active, click an atom to set it to the active element. Clicking a carbon while carbon is active toggles its label visibility instead.
  • Hover-type. With the Select tool active, hover an atom and type an element symbol (1 or 2 letters, e.g. Cl, Br). The full placeholder set R, X, A, M, L, Q, Y, Z, D, T is accepted too, optionally with trailing digits (R1, X2). Enter commits immediately, Esc cancels and restores the previous label; otherwise the change commits half a second after you stop typing.
  • Label editor. Double-click an atom (or click it with the Text tool) to open an inline rich-text editor for a custom label. Enter saves, Esc reverts, and Shift+Enter inserts a line break for multi-line labels. Bold, italic, subscript, and superscript formatting are available while editing.

Label styling beyond the text itself (size, weight, color, halo) lives in the Object Properties Panel.

Implicit hydrogens

Molkit can display implicit hydrogens on labeled heteroatoms (for example OH, NH2), with the count derived from standard valence adjusted for bond order and charge. This display is off by default; turn it on with Structure, then Display, then Show Implicit Hydrogens. The H text is placed on the side opposite the atom’s bonds: left or right is preferred, with above or below used only when the bonds run strongly vertical. Isolated atoms default to H on the right. Override the automatic placement per atom via the right-click “Aux Position” submenu (Auto, Left, Right, Above, Below) or the Properties panel. Implicit-H custom labels such as CH3 are mirrored to H3C when bonds approach from the right, so the bonded element stays adjacent to the bond.

See also