3D optimization and keyboard drawing

3D optimize… (Cmd/Ctrl+Shift+D) generates a molecular conformer and lets you adjust its projection before applying it. Select and Lasso combine mouse and keyboard drawing by default: a visible hotspot is the target for contextual letters, digits, and arrow navigation. v draws a three-member ring, and l enters Cl at an atom or empty hotspot. Choose Select/Lasso with the tool buttons; Escape cancels the current operation or returns to Select. F8 switches the current tab between hotspot drawing and classic contextual controls. Commands that do not fit in the context row are in its ⋯ menu.

Preview an optimized molecule

The preview opens the right Properties panel. Force-field, pin, view, and depth controls scroll there; Apply and Cancel remain at its bottom. The canvas toolbar stays one row, with a 3D preview → link that reopens the controls if the panel is hidden or showing another tab.

1. Select an atom, a bond, or the whole molecule, then press Cmd+Shift+D on macOS or Ctrl+Shift+D on Windows/Linux, or choose 3D optimize…. A partial selection still includes its entire connected molecule. With no selection, the drawing must contain exactly one molecular component.
2. Wait for the initial conformer. Three mutually exclusive buttons choose MMFF94, MMFF94s, or UFF; the selected button is checked and the default is MMFF94s. If generation fails, choose another field to regenerate, or use Generate 3D to retry the current field. Missing parameters produce an error; ReShiki does not silently change the chosen field.
3. Use Start relaxation to enable live local relaxation. Drag an unpinned atom to move it while the rest of the molecule relaxes around the target. Dragging retains that atom’s current displayed depth. Stop relaxation stops calculation and keeps the preview. You can move targets while stopped, then press Start relaxation to relax from the latest target. A converged live session shows Live relaxation ready and waits for another edit.
4. Shift-click atoms to add or remove them from the selection, then choose Pin selected. Pins hold exact physical XYZ positions during relaxation. Use Unpin before dragging a pinned atom, or Clear pins to release them all. A partial selection made before opening the preview is pinned at its newly generated positions; selecting the whole molecule starts with no pins.
5. Rotate with the 3D tilt tool by dragging an atom or inside a ring, or use the preview controls ↶, ↷, Tilt up, Tilt down, and Roll. Switch back to Select for atom dragging and Shift-click selection. Rotation changes the viewing projection while retaining physical pins and energy. Show original lets you compare the untouched drawing.
6. Choose Apply to validate and commit the displayed projection as one Undo step. Cmd/Ctrl+Z restores the original drawing; Redo restores the applied result. Cancel discards the entire preview. Escape cancels an active atom drag first; with no active canvas gesture, it also cancels the preview.

The committed document stays unchanged until Apply completes. Ordinary graph edits are paused during a preview. Pan and zoom remain available; switching tabs pauses that tab’s calculation. Apply rejects invalid coordinates, extreme bond stretching, atom overlaps, and inversion or degeneration of specified tetrahedral or double-bond stereochemistry.

Force fields and calculation scope

The backend uses the Rust COSMolKit 0.3.0 implementations of ETKDGv3, MMFF94, MMFF94s, and UFF, with its exact source revision pinned by Cargo. The installed application is one executable and requires no Python or RDKit runtime. The independent development comparison uses RDKit 2026.03.6; the embedded parameter sources originate from RDKit 2026.03.1. The source and distribution details are in Rust 3D geometry distribution.

Generation uses a bounded, seeded conformer ensemble, minimizes the valid candidates with the chosen field, and selects their lowest energy result. When a drawing retains valid, genuinely three-dimensional coordinates, those coordinates are optimized first. Flat drawings, including tilted planes, and coordinates that conflict with the specified chemistry use conformer generation. Fullerene cages such as C₆₀ use a short initial trial and a distance-geometry fallback without flat-geometry assumptions when that trial fails. This changes the starting geometry; the chosen MMFF/UFF force field and stereo validation still apply to the resulting molecule. Closed carbon cages must also stay inside the supported near-convex geometry envelope; a folded or strongly nonconvex cage produces a diagnostic instead of being applied. C₆₀ has a full regression fixture; this does not establish support for every larger fullerene. An unsuccessful ensemble dominated by planarity rejections may use that alternate initialization for other strained structures too. If embedding times out, ReShiki may retry with a single conformer. This reduces sampling rather than changing the chosen force field. Retries remain bounded. The preview identifies existing 3D geometry, cage or alternate starting geometry, and single-conformer recovery. Subsequent dragging performs bounded local minimization. An unchanged set of targets and pins pauses after 50 batches or eight batches without meaningful energy improvement. The preview stays editable; moving a target or changing pins resumes live calculation, and Start deliberately retries. Stop keeps calculation stopped until Start. This searches nearby conformations rather than guaranteeing a global minimum. The displayed energy is in kcal/mol; compare it within the same molecule and force field. After switching fields in a stopped preview, press Start to recalculate.

The supported calculation domain is one connected covalent component. Available memory determines admission of 128–640 original atoms, with at most four times as many original bonds and 4,096 all-atom coordinates, including temporary hydrogens. Unknown memory observations retain the 512-atom / 2,048-bond envelope. Larger structures remain editable. See the calculation resource policy for independent safety ceilings and time limits. Supported elements are H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, and I, with valid valence and available parameters for the selected field. Formal charges are limited to −8…+8. Single, double, triple, and aromatic bonds, ordinary tetrahedral stereo, and alkene stereo are supported. Query or variable atoms, radicals, coordination and multi-centre attachments, hydrogen-bond contacts, partial and quadruple bonds, and enhanced or non-tetrahedral stereo are rejected.

Calculation-only hydrogens are added on a detached graph and retained through relaxation. Original atoms keep their IDs and order. These temporary hydrogens are not inserted into the drawing by Apply. The resulting projection keeps the editable document objects and specified chemical stereo; unspecified centres do not acquire new document stereo assignments.

Automatic depth, frozen gray, and original ink

Automatic depth is initially enabled in the preview. Rear atom labels, bonds, and ring fills fade toward the canvas background as the projection rotates; black ink appears gray on a light canvas. Base colors remain editable. Depth appearance changes paint, independently of force-field calculation and chemical bond styles.

Turning Automatic depth off freezes the current fade. It keeps the XYZ projection and visible colors; further rotation does not recalculate the fade. Clear depth removes the fade and restores the base colors while keeping the current projection. Re-enable Automatic depth to make the fade follow depth again. These preview changes are committed only by Apply.

After Apply, Select/Lasso offers Enhance depth, Freeze depth, and Clear depth when applicable. Their ⋯ menu labels are Enhance depth appearance, Freeze depth appearance, and Clear depth appearance. They operate on complete selected molecular components, or all components when nothing is selected. Original ink / Use original ink for selection lets selected atoms and their connecting bonds use their base ink within an otherwise faded molecule. Native documents retain the editable depth appearance; figure and clipboard output use the visible paint.

The Rear opacity control (ReShiki 0.12.0 and later) separately makes rear ink lighter or transparent from Properties → 3D appearance. Its default 100% preserves opaque paint. Clear depth also restores rear opacity to 100% while retaining XYZ.

Draw with mouse and keyboard

Keyboard drawing is on by default in Select and Lasso, including new blank drawings. The marker and context row show the active atom, bond, or empty position. No F8 activation is needed. An initial single selected atom or bond’s two endpoints provide the target; otherwise the nearest visible atom or bond to the view centre is used. A blank drawing initially targets the view centre.

Actual mouse motion or a canvas click transfers the hotspot to the pointed atom, bond, or empty position. Arrow navigation and keyboard edits then retain that hotspot until the pointer moves or is clicked again. A stationary pointer does not pull the hotspot back to an older hover target. Moving to empty canvas also provides a position where a shortcut can start another structure.

Letters and digits reuse the existing atom shortcuts and bond shortcuts. Their chemical mappings are not new shortcuts. On empty canvas, an atom letter creates the first atom, 1 creates a C–C bond, and 3 / 6 / 7 starts phenyl / a six-member / a five-member ring. v attaches or fuses a three-member ring, or seeds one on empty canvas. l enters Cl at an atom or empty hotspot; at a bond it places the double line on the left. These contextual commands take priority over the classic v / l Select/Lasso aliases. Use the tool buttons to choose Select or Lasso, or Escape to cancel/return to Select.

For example, on a new blank drawing, n → 1 → 1 creates an N–C–C chain with the final carbon active. Arrows navigate atom → bond → atom; Shift+arrows skip the other target kind, moving atom → atom or bond → bond. Navigation does not edit the drawing. 1 at an atom grows the chain and advances to its new endpoint; 0 adds a branch while keeping its origin active. Ring attachment keeps the attachment hotspot. Enter opens the active atom’s label draft, even after a ring operation selected several atoms. At a bond or empty hotspot, Enter opens Properties. To name a selected fragment with Contract selection, turn keyboard drawing off with F8 first; classic Enter edits an existing selected abbreviation or contracts a multi-atom selection. With hotspot drawing on, the active atom takes priority over the selection.

For a coordination contact, mark a donor N/O/S/P with [, navigate to a transition metal and use Coordinate } or }. This adds a directed dative contact without moving atoms; ] keeps its ordinary covalent checks. See coordination contacts for scope and projection styling.

To close an open chain, navigate to one endpoint and press [, then navigate to the other endpoint and press ]. This adds a single bond and clears the mark. Self-connections, duplicate bonds, and rejected valence changes leave the drawing unchanged. Committed edits are Undo steps; Undo/Redo also restore the hotspot and connection mark associated with the edit.

Press unmodified F8 or turn off Keyboard drawing in the controls for this tab. This restores classic pointer/selection contextual shortcuts and arrow nudging: arrows move a selection by 1 drawing unit, or 10 with Shift. The opt-out survives tool and tab changes; new tabs start with keyboard drawing on. F8 or the Keyboard drawing command turns it back on and returns to Select. With keyboard drawing off, clear the selection and point to empty canvas to use v / l for Select/Lasso. At a classic atom or bond target, their existing chemical actions still apply. Escape retains ordinary cancel/return-to-Select behavior and preserves the tab’s on/off choice; it is not a persistent off command.

Other drawing tools suspend the hotspot and clear a pending connection mark. Return to Select or Lasso to resume automatically, unless this tab was opted out. Text fields, atom-label drafts, and dialogs retain their typing and caret keys; finish or cancel them before canvas shortcuts. Cmd/Ctrl and Alt retain their usual modified commands. Lowercase and uppercase remain distinct, and Shift+3–8 still selects ring tools.

Reviewer reproduction: keyboard targets and history

Use a new drawing for each empty-seeding case, with Select or Lasso active and no draft or field focused. Do not press F8 to start. Once a keyboard step has chosen the hotspot, leave the pointer still until testing a deliberate mouse transfer. In navigation cases, choose the arrow pointing toward the next visible target; Left, Right, Up, and Down prefer connected targets.

Keys / gesture	Target/setup and short reproduction	Expected result
n; 1; 3 / 6 / 7	In separate new blank drawings, press the shown existing shortcut directly	Create N; a C–C bond with its new endpoint active; or the corresponding ring, without F8 or mouse placement
Arrow / [ / ] / Enter	On a blank drawing, try these before seeding	No graph or Undo entry is created; Enter opens Properties, while navigation and connection keys need a target
Arrow	Seed n → 1 → 1, then press an arrow toward the previous atom twice	Atom → intervening bond → atom; positions and connectivity do not change
Shift+arrow	From the same chain, navigate first from an atom, then from a bond	Atom → atom or bond → bond; the other kind is skipped without editing
Mouse motion / click	Move to or click an atom, a bond, then empty canvas	The hotspot transfers to that atom, bond, or drawing position
Stationary pointer	Move onto one atom, use Shift+arrow to another, then type n without moving the pointer	The keyboard-chosen atom changes to N; the previous hover does not steal the target
1 / 0	At an atom with available valence, press 1; navigate back and press 0	1 advances to the new endpoint; 0 leaves the branch origin active
v / l	Try v at an atom, a bond, or an empty hotspot; try l at an atom or empty hotspot, then at a double bond	v attaches/fuses/seeds a three-member ring; l enters Cl or places the double line left; neither selects a tool while its chemistry action applies
Enter / Escape	Seed a ring with 3 and press Enter with its ring selection intact; press Escape	Only the active atom’s label draft opens; Escape closes the draft and keyboard drawing remains on
F8; Enter	Select several uncontracted atoms, turn keyboard drawing off, then press Enter	Classic Contract selection opens; a fully selected existing abbreviation instead opens its label draft
[	At an open-chain endpoint, press [; repeat at a bond target	Mark the atom without an edit; a bond target only shows the atom-target hint
]	After [, navigate to the other nonbonded endpoint with available valence and press ]	Add one single bond, keep the current atom active, and clear the mark; rejected connections do not edit the graph
Cmd/Ctrl+Z; Cmd/Ctrl+Shift+Z	Undo/Redo a connection, growth, or branch; Windows also accepts Ctrl+Y	Restore the graph, hotspot, and mark for each committed edit; navigation and marking alone add no Undo entries
F8 / Keyboard drawing control	Turn keyboard drawing off, select an atom, and use Arrow / Shift+arrow	Classic 1 / 10 unit nudging returns; tool and tab changes retain this tab’s opt-out
v / l with keyboard drawing off	Clear the selection and point to empty canvas, then press v or l	Classic Select/Lasso tool aliases work; classic atom/bond contextual chemistry remains available at its targets
F8	From an opted-out tab, press F8 again	Return to Select and re-enable hotspot drawing for that tab
Another tool / Escape	With keyboard drawing on, choose a bond or text tool, then press Escape	The other tool suspends the hotspot; Escape returns to Select and resumes it without changing the on/off preference
Escape	Press Escape in Select once with keyboard drawing on, and once after F8 turned it off	Ordinary cancellation preserves each state; Escape does not toggle keyboard drawing

For the optimizer review, select a whole molecule and open 3D optimize…; check each of the three force-field buttons, Start/Stop, Shift-selection and Pin selected, Select ↔ 3D tilt, and Automatic depth off versus Clear depth paint. Finish once with Cancel and once with Apply → Undo → Redo. Expected behavior is described above; these are reproduction steps, not additional platform-validation claims.

ChemDraw’s contextual hotkeys informed this workflow. Its ChemDraw 21 manual documents arrow hotspot navigation with a selection tool and assigns F8 to View → Reduce (zoom out). ReShiki assigns F8 to the per-tab keyboard drawing toggle. ChemDraw remains the reference for contextual chemistry; ReShiki’s default hotspot lifecycle, empty-canvas seeding, branch focus, and [ / ] connection commands follow the contract above. This is not an exact ChemDraw clone. Revvity’s ChemDraw tips and tricks guide provides further contextual shortcut examples.