Draw with the assistant

First time using the assistant? Install Codex and connect your account. Codex is optional for ordinary drawing. See the illustrated 0.8 changes for ligand, clipboard and drawing improvements.

Describe the drawing

Open Assistant, describe the structures and their arrangement, then Send. For example:

Draw the esterification of acetic acid and ethanol. Put the reactants on the left, ethyl acetate and water on the right, and acid catalyst above the arrow. Keep carbonyl groups upright and align the reaction horizontally.

The assistant receives your request and drawing context and uses the document’s drawing style. It needs a Codex connection and internet access. Ordinary drawing and local chemistry work without the assistant.

Draw from an image

Copy a chemical drawing, click the assistant prompt and press Cmd/Ctrl+V, or choose ＋ → Paste image on macOS or Windows. ＋ → Choose image… also accepts PNG, JPEG, TIFF and WebP files on every platform.

Pasting attaches the image and shows its thumbnail. Add instructions, then choose Send to let the AI agent draw the molecular structures. You can also send just the image. The assistant compares its drawing with your source before offering an editable preview. ＋ → Remove attached image clears the source; New conversation also clears it. Text-only paste works normally.

Ordinary molecules use the local chemistry engine. Projected organometallic structures can be rebuilt as grouped, editable diagrams. Ring-centre contacts use editable centroid anchors and dashed drawing bonds. These diagrams require explicit review and are not validated molecular data for chemistry export. Inspect the result, then Apply; Undo restores your previous drawing.

Source images are sent to Codex for reconstruction and review. Supported inputs are up to 16 MB and 16 million pixels, with at most 8192 pixels on either side.

Sent images stay with their user messages during the current conversation, even after the composer attachment is removed. Click a thumbnail to enlarge and inspect it. History is session-local and does not survive an app restart.

Transparent source images are composited onto white in the copy sent to the model, so black bond lines remain readable. The original remains unchanged.

A five-minute inactivity timeout renews with relevant progress; each model turn has a twenty-minute hard limit. Connection setup has a sixty-second limit. Completed previews remain available after interruption.

Follow its progress

Preparing your scheme…, an elapsed timer, and Stop appear immediately. The activity card then shows a composition outline, completed structure counts, an editable draft preview, and the quality-check stage. During a quiet model response, the timer remains visible; the app does not invent a completion percentage.

Keep drawing, dragging, zooming, or typing while generation runs. Closing the panel keeps the job running; Assistant · Working in the toolbar lets you return to it. Intermediate drafts stay in the conversation. They do not repeatedly change your canvas.

Opening composer menus keeps your place in the conversation. After reading earlier messages, use Jump to result to return to a completed draft. Reopening the panel restores your previous position.

Stop ends the request and retains any completed preview. You can inspect or discard it, edit its layout, or ask the assistant to improve it.

Choose an arrangement

Describe the roles of the parts as well as the chemistry:

Arrangement	Example request
Aligned rows	“Put these three reactions in rows with aligned arrows.”
General reaction and examples	“Put the general reaction in the center, with Triolein and Tributyrin as separate examples.”
Labeled grid	“Arrange these related reactions in two columns, with a caption for each.”
Branching reactions	“Put acetaldehyde in the center, reduction to the right, and oxidation above it.”

ReShiki measures the actual structures and captions to place the panels. Compound names share a baseline within each horizontal reaction row. Bond lengths remain consistent, and the assistant can rotate molecules in 30-degree steps to make carbonyls upright. Branching currently supports one shared reactant with several outgoing reactions.

Ask for compact long chains when they would overwhelm the figure. The underlying atoms and bonds remain editable and can be expanded again. Ask to preserve full structural detail when the complete chain should stay visible.

Inspect and adjust the preview

Use Overview to see the composition, or select a reaction or molecule to inspect it more closely. Draft controls let you move parts and adjust arrow lengths. Editing an intermediate draft stops generation so the assistant cannot replace your adjustments.

Before a draft can be accepted automatically, the assistant reviews an overview and reaction close-ups alongside your request and the editable object data. It can correct spacing, alignment, captions, arrow length, and compact representations. Each changed version is rendered again. Local checks also look for layout problems and applicable chemistry constraints.

Corrections are bounded. If review fails or problems remain, the preview keeps the findings visible for your decision. Inspect the chemistry before using a generated figure.

Apply or improve

Mode	What happens
Review edits	Inspect the draft, then Apply or Discard it.
Accept all edits	Apply automatically only after the exact final draft passes review with no unresolved findings.

Use Review → Replace selection to replace the selected part. Changes made while generation runs are protected from being overwritten by an older proposal. Applying a draft is one Undo step in either mode.

Ask for a follow-up, such as “Move the conditions above the arrow,” or use Improve on a draft, selection, or existing drawing. The assistant reviews the rendered result and proposes editable layout changes.

Choose a model

The assistant defaults to GPT-6 Astra when it is available in your Codex account. If it is unavailable, ReShiki uses your account’s default model. Choosing a model explicitly saves that choice. Open the effort menu to choose reasoning effort and service tier. Defaults are Low and Standard.

Projected structures and attachment points

Select ring atoms and choose the left 3D tilt tool. Drag vertically for X or horizontally for Y; hold Shift for 15° snapping. Right-click → 3D tilt… and the tool’s context row also offer 15° X/Y steps; Properties → Transform → More takes exact tilt angles. The opposite step restores the geometry; labels remain upright. Aromatic circles follow the ring automatically. Select a separately drawn ellipse with the ring to tilt them together. Emphasize front bonds uses depth to bold foreground single bonds without assigning wedge stereochemistry.

Add centroid creates a selectable ring-centre anchor with an editor-only marker that follows the selected atoms. A dashed contact can connect that anchor to a metal. Dummy atom (*) places an explicit wildcard attachment point; it is not a carbon atom. Native ReShiki files preserve centroids and projection depth. Figures preserve their appearance. Molecular export of centroid diagrams is blocked because these drawing contacts do not encode validated multicentre chemical bonds.

Typed multi-center and variable attachment points are available separately; they retain all-target or alternative-target meaning through supported exchange. A legacy drawing centroid is never silently promoted to either type. See attachment comparison. The assistant can use these operations while reconstructing an image, keeping flat drawings flat unless perspective is visible or requested. Such diagrams always require manual review before applying.

Native/figure output retains front-bond emphasis. CDXML/CDX rejects that emphasis until it can be preserved without being interpreted as stereochemistry; turn off Front bonds for supported editable export.

For Cp/Cp*, the assistant builds the defined aromatic ligand before applying 3D tilt: Cp retains C₅H₅⁻ and Cp* retains C₁₀H₁₅⁻ with five methyl groups. The inner circle follows the ring plane; front-edge emphasis leaves methyl bonds thin. Review can adjust one attached ligand and its contact overlap without moving the metal or other ligands. Zero tilt leaves the ligand planar. These operations preserve the encoded ligand data; they do not validate the complete complex.

Changing or reversing an aromatic ring wedge now preserves its aromatic order and inner curve. Single restores the plain appearance. Partial inner curves no longer show extra dashed aromatic edges. To hide a charge symbol while retaining its stored formal charge, use Properties → Labels & chemistry → Atom labels & numbering… → Show charge labels for the desired scope. Native and figure exports retain this appearance; CDXML/CDX currently requires visible charges and rejects unsupported aromatic projection wedges.

The prompt shows about six lines before it scrolls. An attached image’s thumbnail appears below it, sized to the picture’s shape so wide schemes stay legible; click it and choose View image to enlarge it. Use ＋ for attachments, the model menu to change models, and Review for replacement and automatic-application settings.

Ring shortcut

Shift+R toggles saturated/aromatic ring drawing while retaining the current member count. With the Select tool and one complete 3–8 member ring selected, the same shortcut converts that ring in place. Atom positions, attachments and charges are preserved; Undo restores the original bonds. The aromatic drawing mode does not infer charges or establish chemical aromaticity. To toggle an existing aromatic ring’s circle/alternating-bond display, select the complete ring, move the pointer off atoms and bonds, and press lowercase a.