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Molkit

Fischer Projection

A Fischer projection draws a molecule as a vertical carbon backbone with horizontal substituent pairs at each stereocenter. Molkit builds it from real atoms and bonds linked to a projection object, so you can edit any substituent while the layout stays locked to the Fischer convention.

Place a Fischer projection

Open the projection tool flyout in the toolbar (or press J to activate the projection tool) and pick one of the Fischer variants: 1, 2, 3, or 4 centers. Click the canvas to place it. Molkit creates the vertical backbone, a horizontal H substituent on each side of every center, and terminal groups above and below, then switches back to the Select tool with the new projection selected.

Center carbons are hidden by default; the horizontal arms and vertical backbone render as plain lines.

Edit substituent labels

Double-click any substituent or terminal atom to open the atom label editor and type a new group such as OH, CHO, or CH2OH. Simple element symbols (H, O, N, halogens) are stored as that element; compound labels become carbon atoms with a custom label.

Add or remove backbone carbons

Two ways:

  • Properties panel. The Centers row in the Layout section shows the current count with + and - buttons. + appends a center at the bottom; - removes the bottom center.
  • Right-click menu. Right-click a selected projection atom to get “Add center above”, “Add center below”, and, when the projection has more than one center, “Remove this center” for the center you clicked.

Removing a center bridges its vertical neighbors and deletes its horizontal substituents. The last remaining center cannot be removed. After any change the projection relayouts to even spacing.

Projection Properties panel

Selecting any atom in the projection opens the Projection Properties panel:

  • Spacing and Arm Length sliders control vertical center spacing and horizontal arm length (10 to 80 px, default 40).
  • Thickness and Color set the line weight and stroke color.
  • Crossing chooses Continuous (lines drawn straight through each center) or Break (small gaps in the vertical line at each crossing).
  • Show center C displays the backbone carbon labels.
  • Show R/S labels draws the R/S stereo label at each center that has one assigned. Assign labels per atom; see the stereo labels page.
  • Numbering numbers the backbone carbons: None, Top to Down, or Bottom to Up.

Double-click any slider to reset it to its default.

See also