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Molkit

Right-Click Menus

Right-clicking the canvas opens a context menu built for whatever sits under the cursor. The click selects that object first, but if the object is already part of a multi-selection, the selection is preserved and the menu applies to the whole group. Right-clicking empty space keeps your current selection. Only items relevant to the current selection appear.

Right-click drag pans the viewport instead of opening a menu (see Navigation). The menu can be driven from the keyboard: the arrow keys move between items, Enter runs one, and Escape closes it.

Empty canvas

With nothing selected, the menu offers Paste, Select All, Zoom to Fit, Grid Settings…, and Page Setup….

Any selection

These items lead the menu for nearly every selection:

  • Properties… (P) opens the matching properties panel when atoms, bonds, lone pairs, radicals, or orbitals are selected (see Object Properties).
  • Cut, Copy, Paste, Duplicate, and Delete, the same commands as the Edit menu.
  • Flip Horizontal and Flip Vertical mirror the selection across its bounding box (when it includes atoms or annotations).
  • Name Selection… saves the selection as a named selection and opens the metadata editor so you can name it. If the selection already is a named selection, the item reads Edit Metadata instead. See Named Selections.

Further down, most selections also get:

  • Bring to Front (Ctrl+Shift+]), Bring Forward (Ctrl+]), Send Backward (Ctrl+[), Send to Back (Ctrl+Shift+[) reorder the object within the stack (see Layers and Groups).
  • Group (Ctrl+G) when two or more items are selected; Ungroup (Ctrl+Shift+G) when a group is selected.
  • Copy as Image (Ctrl+Shift+C) puts a rendered image of the selection on the system clipboard.
  • Export Selection as SVG… / Export Selection as PNG… export only the selected objects (see SVG Export).

With View > Single-Pointer Editing turned on, the menu adds Move Selection (atoms only), Rotate Selection, and Resize Selection, which move, rotate, or scale the selection with clicks instead of a drag. See Keyboard Shortcuts.

Atoms

  • Flip Selection and Detach Selection (the second only when the selection is part of a larger molecule) mirror or cut free a piece of a molecule; see Arrange.
  • Straighten Bonds puts bonds that are slightly off a 15 degree line back on it, in the molecules the selected atoms belong to (see Bond Tool).
  • Aux Position submenu (Auto, Left, Right, Above, Below) moves the auxiliary text relative to the atom label (see Atoms and Elements).
  • View 3D Structure (when you right-click an atom) opens the 3D panel for the molecule that contains it (see 3D Structure Viewer).
  • Set Element Color… (single atom) opens the color scheme editor focused on that element.
  • Expand “[label]” on a collapsed abbreviation atom; Collapse to Abbreviation… on a multi-atom selection (see Abbreviations).
  • Set Atom Number… on a single atom; Number N Atoms (1, 2, 3…) numbers a multi-atom selection in the order you selected it; Clear Numbers from Selection removes them (see Atom Numbering). To clear the numbers from every atom at once, use Structure > Atom Numbering > Clear Atom Numbers with nothing selected.

Generic groups (single atom):

  • Convert to generic group turns the atom into a generic placeholder labeled R (or its current custom label). A generic atom has no fixed element.
  • On a generic atom, Define R-groups… opens the list of substituents that atom can stand for, and Convert to regular atom turns it back into carbon.
  • Save as R-group substituent appears when two or more atoms are selected and you right-click one of them. It saves the drawn fragment to the document’s R-group palette. Mark where the fragment attaches first: either draw a squiggle across the attaching bond (see Add attachment point under Bonds) or right-click the attaching atom itself. Only one attachment point is allowed.

Views and sets (see Views and Resonance):

  • Generate resonance forms appears for a symmetric ion with one delocalized pi bond, such as carbonate, nitrate, or a carboxylate. It draws the other equivalent forms next to the one you drew.
  • Generate octet resonance forms appears for an expanded-octet species such as SF6, PF5, or XeF4. It draws octet-respecting ionic forms.
  • Mark as Resonance Set groups two or more drawn forms joined by a resonance arrow into a resonance set; Unmark Resonance Set turns it back into a plain named selection.
  • Group as Visual Set groups depictions of one species in different views (for example a Lewis structure and a VSEPR drawing) into a Visual Set; Unmark Visual Set removes the set.
  • Show under Lewis & VSEPR (planar) and Show under Lewis only switch a planar resonance set between counting as both views and as Lewis only.
  • Set category submenu tags a single structure with its view: Lewis, Lewis (square), Lewis (angled), VSEPR, Condensed, Bondline, Fischer, and, for a planar species, Lewis + VSEPR (planar). The active category carries a check mark; click it again to remove the label.
  • Derive view submenu draws the structure in another view: Lewis (or Lewis (angled) and Lewis (square) when both layouts differ), Bondline, Condensed, VSEPR, Fischer projection, Orbital picture (a copy with an orbital picture built on it), and All applicable. Only the views that make sense for the structure are listed.

In animation mode:

  • Set as Animation Center (or Set N Atoms as Animation Center) marks the selected atoms as the alignment center; Clear Animation Center removes it (see Animation States).
  • Match Charge Pos from Prev State / Match Charge Pos from Next State copy a charge’s custom offset from the adjacent state (see State Matching).
  • Preview Bond Formation appears when exactly two atoms that each carry a radical are selected, and plays a short preview of the two radicals forming a bond.

Orbitals submenu (single atom): Fill with sp, Fill with sp², Fill with sp³ replace the atom’s orbitals with a hybrid set, and the one that matches the atom is marked “(recommended)”. Existing orbitals on the atom are replaced; a warning tells you how many, and Ctrl+Z restores them. A single selected orbital also gets Hold Lone Pair or Release Lone Pair, as long as Structure > Display > Hybridization Tools (Experimental) is checked (it is by default for new documents). See Orbital Lobes.

Bonds

When two bonds cross, these control which one draws on top:

  • Bring Bond to Front paints this bond over crossing bonds.
  • Send Bond to Back paints it underneath.
  • Reset Bond Crossing Order (shown only after you customize) restores the default order.

With a single bond selected:

  • Add attachment point draws a point-of-attachment squiggle across the bond, at its terminal end; Clear attachment point removes it. The squiggle marks where a fragment connects when you save it as an R-group substituent (see Squiggle Line).
  • Draw orbitals: σ only, Draw orbitals: σ + π (double), and Draw orbitals: σ + 2π (triple) draw an orbital framework for the bond when Hybridization Tools (Experimental) is checked, which it is by default for new documents; the one that matches the bond order is marked “(recommended)”.

Arrows

Curved and multi-segment arrows carry the largest menu (see Arrow Beautification and Curved Arrows):

  • Beautify applies the full automatic cleanup pass.
  • Auto S-Curve and Auto Shape fit the curve to a standard profile.
  • Flip Curve (F) mirrors the bow to the other side.
  • Straighten, Symmetrize, and Smooth Curve adjust the existing shape.
  • Align to Dots (spline arrows) lines the curve up with its electron-source dots.

Waypoint editing on multi-segment and spline arrows, when you right-click near a waypoint:

  • Delete Point (Del) removes the waypoint under the cursor.
  • Add Bezier Handles / Remove Bezier Handles toggle tangent handles on a waypoint.

Attached-arrow tip control (see Curved Arrows):

  • Reset Tip to Bond Midpoint clears a slid tip position on a bond-anchored arrow.
  • Flip This Tip to Other Side (spline) moves the tip approach to the opposite side.
  • Reset Head to Perpendicular (edge-attached spline) restores the default head angle.

With exactly two arrows selected:

  • Mirror Curve to This / Mirror Curve from This copy one arrow’s curve shape onto the other, mirrored.

Special annotations reuse the same menu:

  • Edit LaTeX Equation… reopens the editor for a LaTeX annotation (see LaTeX).
  • Edit Chart… reopens the chart editor for an imported chart (see Imports).

Text

  • Shrink to Text tightens a fixed-size box to its content.
  • Make Auto-size returns the box to automatic sizing (see Text).

While you are editing text, right-clicking inside the text box opens an editing menu instead: Cut, Copy, Paste, Paste as plain text (Ctrl+Shift+V), Select all, Insert symbol…, and Clear formatting.

Standalone lone pairs and radicals

Free-floating lone pair and radical annotations get two submenus (see Lone Pairs):

  • Representation: Dots, Lines, or Lobes.
  • Color Mode: Standard or Custom Color.

Net dipole arrow

Right-clicking a molecule’s net dipole arrow opens a short menu: Reset dipole position moves the arrow back to its default place, and Hide dipole turns it off for that molecule (see Net Dipole).

Projections

  • Fischer: Add center above / Add center below extend the backbone; Remove this center deletes the clicked stereocenter (see Fischer).
  • Chair: Flip Chair performs a ring flip (see Chair).
  • Newman: Set Conformation submenu with Staggered (60°), Eclipsed (0°), Anti (180°), Gauche+ (60°), and Gauche− (300°) (see Newman).

Animation annotations

Inside animation mode the menu adds (see Animation States):

  • Propagate to All States adds the selected annotation to every state it is missing from.
  • In the LaTeX animation workspace, Show for whole state makes the selected annotations appear when a state settles and stay until the end of its step, and Timing… opens a small timeline for fine-tuning when they appear and disappear.
  • On a LaTeX state box, Delete animation… deletes the whole LaTeX animation after confirming. State boxes cannot be deleted one at a time.

While the Match Editor is active, the canvas context menu is suppressed.

Tab bar

Right-clicking a document tab opens its own menu: Close Tab, Close Other Tabs, Close Tabs to the Right, Duplicate Tab, and Close All Tabs (see Tabs, Auto-Save & Recovery).

See also