Stereochemistry Labels

Stereo labels are small text markers, R or S next to an atom and E or Z next to a double bond, drawn in red by default. Molkit stores them on the atom or bond, so they move with the structure and survive saving and copying. The labels are descriptive only: Molkit does not run a CIP priority analysis, so you decide the assignment and Molkit draws it. The stereochemistry itself lives in your wedge and dash bonds (see Bond tool); labels sit on top as annotation.

Label a stereocenter

Make sure labels are enabled: Structure, then Show Stereo Labels.
Select the atom. A Stereochemistry section appears in the Object Properties panel.
Pick a label from the dropdown (R, S, r, s, RS, E, Z, M, P, re, si) or type any short text into the field. Choose None or clear the field to remove it.

The same section works on a multi-atom selection to label several centers at once.

Label a double bond

Select a double bond and use the Config dropdown (None, E, Z) in the bond section of the Object Properties panel. The label is drawn near the bond midpoint, offset to one side. It only renders on bonds of order 2; if you later change the bond order, the label disappears until the bond is a double bond again.

Placement and appearance

By default each atom label places itself automatically: Molkit scores the eight positions around the atom (top, bottom, left, right, and the four diagonals) against bond directions, implicit hydrogen labels, charges, and atom numbers, then picks a clear spot. The position is recomputed on every render, so labels keep avoiding clutter as you move atoms or add bonds.

To override placement on one atom, use the Position dropdown in the Stereochemistry section, or simply drag the label with the Select tool; dragging stores a custom offset that follows the atom. Color and size are also per-atom in the same section, with a reset button to return to the document default.

Showing and hiding

Structure, then Show Stereo Labels toggles every stereo label in the document at once. Hidden labels stay stored on their atoms and bonds. Fischer projections have their own Show R/S labels checkbox in Structure Settings and display the same per-atom labels at each crossing.

Limitations

Label text never recomputes. If you swap substituents or flip a wedge, an R label stays R until you change it. Verify labels after editing.
The Structure menu items Assign R/S, E/Z and Clear Stereo Labels are placeholders for a future automatic assigner and currently do nothing.
SMILES import reproduces stereochemistry mainly as wedge and dash bonds and double-bond geometry. The fallback parser (used when the RDKit engine is unavailable) adds E/Z labels from directional markers in the input and places a wedge or dash at each marked center, but the wedge direction is a marker of “this is a stereocenter,” not a CIP-verified depiction. Treat imported stereo as a starting point and check it.