Draw Your First Molecule in ChemStitch

What you'll accomplish

By the end of this guide, you'll have drawn a molecule on the ChemStitch canvas, edited atom labels, applied a ring template, and used keyboard shortcuts to speed up your workflow. No installation required — everything runs in your browser.

Step 1: Open the editor

Sign in to ChemStitch and you'll land on the editor with an empty canvas. If this is your first time, a brief onboarding tour highlights the canvas, chat panel, and key toolbar controls.

The toolbar sits along the top of the canvas. The AI chat panel is on the right side. You can toggle focus between them with Tab.

Step 2: Draw bonds

Click on the canvas to place your first atom, then click again to draw a bond to a second atom. By default you're drawing single bonds.

Switch bond types with keyboard shortcuts: press 1 for single, 2 for double, 3 for triple bonds. You can also select bond types from the toolbar.

For stereo bonds, select wedge (stereo up) or dash (stereo down) from the toolbar. These are essential for representing chirality in drug molecules and natural products.

Step 3: Edit atom labels

Click on any atom to change its element label. Type the element symbol (N, O, S, Cl, etc.) and press Enter. The editor validates your labels and flags valence errors — for example, a carbon with five single bonds will show a warning.

Atom label editing is how you convert a generic carbon skeleton into a real molecule. Start with the carbon framework, then change atoms to heteroatoms where needed.

Step 4: Use ring templates

Press R to open the ring template selector. Templates are organized into categories: Rings, Functional Groups, and Common Molecules. Use the search field to find templates by name.

Each template shows a preview before placement. Click a template and then click on the canvas to place it. You can fuse rings by placing a template on an existing bond.

Step 5: Clean up your structure

Click the clean button in the toolbar to auto-format your drawing into a clean 2D layout. This adjusts bond angles, atom spacing, and ring geometry without changing the molecular identity.

Auto-cleanup is especially useful after building complex structures by hand. It transforms rough sketches into presentation-ready structures.

Or start with a quick-start molecule

If you prefer to skip drawing from scratch, use a quick-start template. The editor offers pre-built structures for benzene, aspirin, and caffeine. Click one to load it onto the canvas and start exploring.

Quick-start molecules are a good way to try out the AI chat features without spending time drawing first.

Tips for efficient drawing

• • Use keyboard shortcuts — Pressing 1/2/3 for bonds and R for rings is much faster than clicking toolbar buttons.
• • Build the skeleton first — Draw the carbon framework, then change atom labels. This mirrors how most chemists think about structure.
• • Undo freely — Ctrl+Z undoes your last action. Ctrl+Y redoes it. There's no penalty for experimentation.
• • Auto-save — Your work saves to the cloud automatically. The status indicator in the header shows Saved, Saving, or Error.