Label atoms and structures

Write a caption

Choose Text (t, lowercase), click the canvas, and type. Double-click a caption to edit it. Select a text range to change its font, size, bold/italic, subscript, superscript, or color. Done or Cmd/Ctrl+Enter applies; Escape cancels.

Number atoms

For atom numbers, hydrogen placement, and stereochemistry labels, use Properties → Labels & chemistry → Atom labels & numbering…. Select an atom to change charge, isotope, radical electrons, or the singlet/triplet spin state of a two-electron atom under Atom details.

Atom numbers are placed automatically on the open side of their atom, clear of bonds, labels and captions. A longer custom number, such as 12a or Cα, starts beside the atom and extends away from the structure. Drag a number with Position numbers & stereo labels to place it yourself; that position is kept.

Adding a charge to a skeletal carbon leaves the carbon label implicit. The charge remains visible at the vertex. Explicit carbon-label settings, isotope labels, and isolated atoms remain visible.

Change OH to HO

You can choose which side of an oxygen atom displays its hydrogen—for example, to change OH to HO.

1. With Select / move, click the oxygen atom you want to adjust.
2. Open Properties → Labels & chemistry → Atom labels & numbering….
3. Set the scope to Selected atoms and check that only one atom is in scope.
4. Under Hydrogen position, choose Left for HO or Right for OH.

Choose Automatic to let ReShiki determine the placement from the surrounding bonds. Keep Show implied hydrogens enabled to display the hydrogen.

This changes the label’s appearance only. The bonds and stereochemistry stay the same. Use Selected atoms to adjust one hydroxyl; Whole drawing applies the setting throughout the drawing. Cmd/Ctrl+Z undoes a placement change.

The screenshots show the same sugar drawing with only the selected hydroxyl’s hydrogen placement changed. Click or tap either screenshot to view the controls at full size.

Right: OH

Left: HO

Open the editable example to try Left, Right, and Automatic.

Shorten a group

Select an atom and press Enter to edit its label. Automatic recognizes elements and defined groups; Chemical abbreviation chooses a nickname explicitly, including names that conflict with element symbols. Text label keeps literal text such as M, L or X on a wildcard atom. Text labels do not imply an element, query or molecular formula.

A group’s reverse spelling also makes the group: MeO gives OMe and BnO gives OBn, shown in whichever spelling suits the side the bond leaves from. NC and OCN make CN and NCO only on a left-hand end, where they read toward the bond; elsewhere they would mean an isocyanide or a cyanate, so they stay text. A group typed over a label that reads to the left, such as a sugar’s HO, keeps that side: OBn there reads BnO. Full names such as morpholino or acetyl stay text; the editor suggests the label to type, such as “Did you mean Morph?”.

Free text labels such as M2+, R1 or L2 are drawn with subscripted counts and a superscripted trailing charge, as in ChemDraw: R1 appears as R₁, M2+ as M²⁺, and SO4 2- as SO₄²⁻. The label keeps the text you typed, and the styling adds no chemical meaning.

Use Properties → Labels & chemistry → Chemical abbreviations… to replace a terminal group with a preset such as OMe, or contract a selected fragment. Expand selected restores its atoms for editing.

Defined groups such as Boc retain their full atom/bond graph for composition. Cp is cyclopentadienyl (C5H5−); Cp* is pentamethylcyclopentadienyl (C10H15−). Their attachment handles are not counted as atoms. Metal charge still needs the correct explicit assignment.

Group labels default to Automatic alignment. Select groups and use the existing top Left / Center / Right buttons; the adjacent menu restores Automatic or selects Above. Captions share those buttons, and mixed selections update together. Alignment never changes the group’s atoms or bonds. Above positions one nickname above its anchor rather than stacking arbitrary formula tokens.

Type formulas and explicit hydrogens

In the atom label editor, type a supported formula such as C2H5 or OCH3. Automatic mode creates a chemical group with real atoms; its digits display as subscripts. Select several atoms and press Enter to give that fragment a group name. Use Text label only when you want literal, chemically unspecified text.

An explicit NH3 label retains three hydrogens. At a metal, its donor contact can be represented without changing it into NH2. These explicit hydrogens participate in molecular properties; labels are not merely decorative. This does not turn off chemical validation.

Group and template definitions may be revised in future releases. Open the shortcut examples to try the current groups in one editable document.

Type a charge on an atom

Select an atom, press Enter, and type the element with its charge, such as Pd2+, Pd+2, Na+ or Cl-. In Automatic mode, this sets the element and its charge, and the charge is drawn as a superscript. Charges go from -8 to +8.

A charged label gets no automatic hydrogens. Type the element alone to restore them. Choose Text label to keep the text exactly as typed.

ChemDraw reads Pd2+ as two palladium atoms; ReShiki reads it as one Pd²⁺ because a single atom cannot be two atoms.

Format part of an atom label

Select characters in the label box and press Cmd+- for subscript or Cmd++ for superscript (Ctrl on Windows and Linux; Cmd/Ctrl+= also works). You can also use X₂ and X² under the box. Plain (Cmd/Ctrl+T) removes the formatting. With nothing selected, the change applies to the whole label. Once you format characters, Appearance under the box shows the result.

In Automatic mode, Pd with a superscripted 2+ becomes a palladium atom with charge +2, and NH with a subscripted 4 and a superscripted + becomes ammonium. Other formatted text, such as M with a superscripted 2+ or R with a subscripted 1, stays a text label with your formatting. Text label always keeps the text and formatting as typed. Chemical abbreviations and group labels cannot be formatted.

To format a whole text label without opening the editor, select its atom and use x₂ or x² in the Style bar.

The formatting is saved in the .rsk file and copied to ChemDraw files. Formatted text labels in ChemDraw files keep their formatting when you open them.

Bond to a text label

You can draw a bond from a short caption, such as Pd²⁺ typed with Text, as you would from an atom. Choose Single bond or another bond tool and drag from the caption’s letters. The caption becomes an atom label and keeps its font, size, and color. Pd²⁺ becomes a palladium atom with charge +2; other formatted text, such as M²⁺, stays a text label with its formatting.

Click the caption to add a bond in the default direction. A bond can also end on a caption. Straight chain and Snaking chain can start from a caption too. Hydrogen bond does not convert captions.

When you point at a caption with a bond tool, the status bar says whether it can become an atom label. Captions with more than one line or more than 32 characters, molecule names, and reaction conditions stay captions. One Undo restores the caption and removes the new bond.

Choose where a bond meets a text label

A bond meets the attachment atom inside a multi-atom text label, not the middle of the label. In MeO, AcS, BnO or SPh the bond meets the O or S; nicknames such as Me, Ac, Bn and Ph, hydrogens and counts never take the bond, even when they spell an element symbol (Ac). When a label names several atoms, the bond meets the one nearest it: CO2Me attaches at C with the bond on its left, and MeO2C attaches at C with the bond on its right. Text that names no atom, such as Boc or M, stays centered, and so does text spelled for the other side, such as MeO with its bond on the left, so the bond is not hidden behind Me. Type OMe for that direction. A text label inside a chain, with two or more bonds, also stays centered unless you choose otherwise. Chemical groups such as OAc or CO2Me typed in Automatic mode always attach at their real anchor atom and switch to their reverse spelling (AcO, MeO2C) as needed.

To choose differently, select the atom and open Properties → Labels & chemistry → Atom labels & numbering…. With Selected atoms as the scope, use Bond attachment (text labels):

• Automatic follows the bonds.
• Flush left attaches at the first atom of the label; Flush right at the last.
• Centered centers the whole label on the atom.
• Character N attaches at exactly that character, for example the M of MeO.

The choice is saved in the .rsk file and applies to the canvas and to SVG, PDF and PNG exports. When you copy to ChemDraw, flush left, centered and flush right are written as label justification, and they are read back from ChemDraw clipboard data and files. Saving a drawing with text labels as a ChemDraw file is not supported yet; a chosen character has no ChemDraw equivalent and is kept only in .rsk files. Editing the label text returns a chosen character to Automatic. Use drawing label defaults also resets it.

Attach to several atoms

Select the target atoms, right-click → Attachment points…, and choose Multi-center attachment for simultaneous participation, such as η6-arene or η3-allyl. Variable attachment represents alternative attachment positions. Draw a bond from the new point to a metal or substituent. These are distinct from a plain dummy atom or drawing centroid.

Anonymous dummy and attachment handles remain visible in the editor but disappear from figures and image copies. Explicit labels remain visible. Native editing retains target IDs; supported editable exchange uses CDXML/CDX attachment nodes or V3000 ALL/ANY lists. See the verified scope and limitations.