Select and refine

Select what to change

Task	Gesture
Select a molecule	Double-click an atom
Select a bond	Click its middle with Select
Select a region	Space, then drag a box; l for lasso
Add / toggle an object	Shift-click
Remove a region	Alt-drag around it
Select everything	⌘/Ctrl+A

Drag a selected object to move it. Drag a corner handle to resize proportionally. Drag a side handle to change only width or height; labels and stroke widths keep their sizes. Use the top handle to rotate freely; Shift snaps rotation to 15°. While you drag, the pointer shows the angle and the step keys. Without the mouse, Option/Alt+←/→ rotates the selection by 1° and Option/Alt+↑/↓ by 15°; plain arrow keys still move it.

Moving a bonded endpoint or collapsed group follows the configured bond length and angle grid. Hold Option/Alt to move freely. Whole molecules move without changing their internal geometry. Whole objects snap their edges, centers and gaps to other objects on screen, and thin magenta smart guides show each match; Option/Alt also moves without guides, and View → Smart guides turns them off.

Hold ⌘/Ctrl while dragging a selection to drop a copy and leave the original in place. Hold Shift to move only horizontally or vertically, or both keys for a copy along one axis. The keys held when you release decide, so to cancel a copy drag, release ⌘/Ctrl first, then press Escape.

Tilt a drawing

Select the atoms, choose the 3D tilt tool on the left, and drag. Vertical movement rotates around X; horizontal movement rotates around Y. Hold Shift for 15° increments. Release to commit one Undo step; Escape cancels the preview. Labels remain upright, and aromatic circles follow the ring.

Right-click a selection → 3D tilt also offers X/Y step commands. A molecule shown only as a 3D model turns its model instead, and its hidden 2D drawing stays as it is (see Show a molecule as a 3D model). The top controls offer Front bonds for depth emphasis and Done to return to selection. Tilt changes drawing perspective, not chemical stereochemistry.

Right-click menus now show relevant commands under Arrange & transform…, Bond appearance… and Attachment points…. Select the objects first to see their actions.

Work with 3D molecules

A MOL file with 3D coordinates keeps them when you open it, so you can tilt the molecule. Ordinary hydrogens become H counts on their atoms. Save a .rsk file to keep the 3D shape; MOL export keeps it too.

To fade the bonds behind the front face of a 3D molecule such as C60, open Properties → 3D appearance. Type a value in Rear opacity and choose Apply. 100% keeps the drawing opaque, and 0% hides the rear bonds. With nothing selected, the setting applies to every molecule. A .rsk file keeps the setting; SVG, PDF and PNG keep the look.

3D optimize… (⌘/Ctrl+Shift+D) builds a 3D shape for one molecule and shows a preview before you apply it. The largest molecule it accepts depends on free memory, from about 128 to 640 atoms.

Show a molecule as a 3D model

Select a whole molecule and right-click it and choose Show as, or open Properties → Structure, below Molecular properties and Labels & chemistry:

• 3D replaces the drawing with a 3D model, ball & stick unless you pick another style.
• Both puts the model beside the drawing.
• 2D shows the drawing again.

The first switch generates the model with the same method as 3D optimize… (ETKDG, then MMFF94s); later switches reuse it. When the model appears, the atoms move from the drawing into 3D and the hydrogens grow out of their atoms. Each switch is one Undo step. The chemistry, atom IDs and your 2D layout never change. Click the model to select its molecule; it then moves, aligns and copies with it.

Editing the molecule’s chemistry keeps the arranged model and shows Structure changed · Update model above the selected model and in Properties → Structure. Choose Update model to generate a conformer for the edited structure. Moving the 2D atoms or changing their appearance does not require an update. Generation runs in the background, keeps the view, frame and appearance, and commits one Undo step when it succeeds. Press Escape to cancel; cancellation, failure or another edit leaves the previous model in place. ReShiki never replaces a conformer automatically.

Splitting or joining structures keeps each arranged model and its surviving atom links. Update model replaces every model linked to the updated molecule with one model, keeping the selected model’s view settings and combining their saved Original drawing layouts. Updating or regenerating requires one connected source structure. If a split leaves the source disconnected, generation reports that limit and keeps the previous model.

Once the model is selected:

• drag inside its frame to rotate it;
• Shift-drag to roll it;
• double-click it to reset the view;
• drag a corner handle to resize it.

Drag the frame’s edge, or a model that is not selected, to move it. The 3D tilt tool and its X/Y step commands also turn a model shown as 3D, the same way as dragging inside its frame, and leave its 2D drawing as it is; anything else selected tilts with it. With Both, tilt turns the 2D drawing. The rotation handle, Rotate 180° and the Rotate field roll a model shown as 3D in place. Flipping, resizing it with Scale, cleaning it up or joining it would change its hidden drawing, so ReShiki asks you to switch to 2D first; in a mixed selection only the other objects flip. Each rotation, tilt and resize is one Undo step.

To go back to 2D, Properties → Structure → 2D layout offers Original drawing, the layout you drew, or From the 3D view, which flattens the model as it is turned now, with far bonds lighter, like 3D optimize…. Show as → 2D from the 3D view in the right-click menu does the same. Each molecule keeps its own choice, and a flattened molecule keeps the layout you drew, so Original drawing brings it back, even after saving and reopening.

When the source chemistry has changed, From the 3D view is unavailable and shows Update the model first. Original drawing remains available.

While the model is shown, Properties → 3D model changes how it looks:

• Style: Ball & stick, Stick (tubes joined with clean mitered joints), Wireframe or Space-filling.
• Look: Flat · journal, with thin outlines (a soft light rim on a dark canvas), or Glossy · slides.
• Hydrogens: All, Polar (on N, O and S) or None.
• Atom labels: None (the default), Heteroatoms (elements other than carbon and hydrogen) or All. Only visible atoms receive labels.
• Depth fade and Perspective sliders.
• Background: None or Soft card.
• Reset view shows the model’s opening view again.
• Regenerate conformer generates a fresh conformer while keeping the view, frame and appearance. It runs in the background, can be cancelled with Escape, and commits one Undo step on success.

The model’s colours follow the drawing’s colour theme (Publication uses the Presentation colours) and the light or dark canvas.

Each change, including one slider drag, is one Undo step.

Models newly imported from crystal and XYZ files keep their imported geometry, including plain XYZ models without a cell or site labels. They do not show the changed-structure message, Update model or Regenerate conformer; their appearance controls remain available.

Older saved .rsk drawings can lack both a chemistry fingerprint and import provenance. ReShiki uses their current chemistry as a baseline and permits Update model and Regenerate conformer, unless a unit cell or file atom sites identify imported geometry. A plain XYZ model saved without those markers is indistinguishable from a generated model. Regeneration can replace its original coordinates, but happens only as an explicit action that can be undone. Reopen the original XYZ file to retain its import provenance.

A .rsk file keeps the model. PNG, SVG and PDF show it as vector shapes. MOL, CDX/CDXML and SMILES contain the 2D structure only. Files saved by this version need this version or later to open.

Keep related objects together

Select a molecule and its caption, then Group (⌘/Ctrl+G). Use Shift+⌘/Ctrl+G to ungroup.

The context row offers alignment, distribution, Flip horizontal, Flip vertical, Rotate 180° and a ° field: type an angle there and press Enter to rotate the selection by exactly that much (positive is clockwise). Properties → Grouping & frames offers Add frame…. Duplicate makes another editable copy.

A fixed Hydrogen position (Left, Right, Above or Below) turns with a flip or rotation, so the H stays on the matching side. At other angles it takes the nearest side. Automatic labels keep following their bonds.

To align a reaction, select its molecules and arrow, right-click, and open Arrange & transform… → Align middles. Each molecule or group moves as a unit. The same submenu offers other edges and even spacing.

Align a bond exactly or stretch one bond

1. Select both atoms of a bond, or a shape with a straight edge.
2. Open Properties → Transform → Reference: align / stretch and choose the bond or edge under Reference.
3. Choose Horizontal or Vertical, or type an angle in Direction and choose To angle. 0° points right and 90° points down.
4. To turn by an angle instead, type it in Turn and choose Rotate. Copy + rotate keeps the original and selects the rotated copy.

Moves chooses what turns: the Connected fragment or only the Selected objects. Pivot chooses the center of the turn. Pin selected center pins the center of the current selection, for example to place copies at 90°, 180° and 270° around it.

To stretch a bond that links two parts of a molecule, type a value in Length and choose Set length, or choose Drag to stretch and drag the moving end along the bond. One end stays fixed; Swap fixed end fixes the other end instead. Everything beyond the moving end moves with it and keeps its shape. Ring bonds cannot be stretched alone.

Each alignment, turn, copy or stretch is one Undo step.

Change color

Select the objects and click the color button in the Style toolbar. Choose All selected, Text, Bonds, or Ring interiors under Apply to, then a swatch. For a custom color, type a hex, RGB or OKLCH value in the Color box and press Return. Edit hues… moves the theme’s hues; the drawing recolors as you go, Done keeps the change as one Undo step, and Cancel or Escape restores the hues.

To recolor matching atoms together, choose Atoms…, select an element and color, then Apply. Choose Selection or Whole drawing; other elements and bonds retain their colors. Undo restores the change in one step.

For a filled ring, select its complete cycle, choose Ring interiors, then a color. The crossed-out swatch at the start of the Tint row clears it. The fill follows the ring during movement, resizing, copying and deletion; it is retained in native files, figures and supported editable exchange.

Join fragments

Select the atoms, then press ⌘/Ctrl+J or choose Join in the context row. In the right-click menu it is Join selected atoms or bonds.

Selection	Result
One atom in each of two fragments	The fragments share that atom
Both ends of one bond in each fragment	The fragments fuse along that bond
Three or more atoms	They merge into the first atom you selected; the other atoms stay put
A donor atom (N, O, S or P) and a transition metal	A dative bond from the donor to the metal is added; neither atom moves

Shift-click to choose the order. When atoms merge, the first atom you select is kept. If four atoms form two bonds, Join fuses the bonds. To merge all four atoms into one instead, choose Merge atoms in the context row or Merge selected atoms in the right-click menu.

For interactive placement, select the fragment and choose Move & attach… above the canvas. Choose its source attachment point and connection mode, then click or drag at the destination to preview and commit the join.

Connect a ligand to a metal

1. Select the ligand and choose Coordinate in place… above the canvas or in the right-click menu.
2. Click the donor atom (N, O, S or P) in the preview, then click the metal on the drawing. Neither atom moves.
3. Repeat for each donor of a chelate. Each contact is one Undo step.

In keyboard drawing, mark the donor with [, move to the metal and press }.

To show the contact as a wedge or hash, choose Solid wedge or Hashed wedge under Properties → Bond appearance → Style. Properties → Crossings & direction → Reverse projection tip narrows the wedge at the other end. Click a plain dative bond again with the Dative tool to reverse it: donor and acceptor swap, the same as Properties → Crossings & direction → Reverse bonds.

Help (?, F1 or Cmd/Ctrl+Shift+/) searches every shortcut by action, key or description and previews atom and bond keys with a before/after drawing. Selecting a row only shows it; nothing runs. Help → Open shortcut examples opens an editable drawing in a Shortcut examples tab in the current window. Opening it again switches to an unchanged examples tab. Save asks for a location for your own copy.

Press : for the command palette: type part of a command, such as benzene, double bond, nmr or :w, and press Enter to run it on the selection or the pointed atom or bond. Each row shows its shortcut. Press Tab / Shift+Tab (or click a chip) to show one category, such as Bond or Insert, and Page Up/Page Down to move a screenful.

Open the complete shortcut reference and editable examples.

Clean up a selection

1. Select a molecule or the atoms you want to adjust.
2. Click Clean up….
3. Compare with Show original, then Apply or Cancel.

Selected atoms keeps the rest fixed. Selected molecules includes each complete molecule touched by the selection. Other molecules stay in place. Keep orientation preserves the drawing’s direction.

Apply is one Undo step. Cleanup adjusts molecular geometry; it does not arrange an entire reaction scheme.

Attachment-containing complexes, including Cp/Cp* groups, retain their geometry with an explicit limitation. Independent ordinary molecules can still be cleaned; unsupported complex geometry is not replaced by a guessed arrangement.