Import Structures from ChemDraw (CDXML)

What you'll accomplish

By the end of this guide, you'll have imported a ChemDraw CDXML file into ChemStitch, understood the stereochemistry warning, and learned how to continue working with your structure in the browser. You'll also know the current limitations of CDXML support.

Why migrate from ChemDraw?

ChemDraw is the established standard for chemical structure drawing, but it requires a desktop installation and a per-seat license (typically $200–$600/year for academic users). ChemStitch runs in your browser with no installation, includes AI analysis tools that ChemDraw does not offer, and is free during beta.

If you have existing ChemDraw files (.cdxml format), you can bring them into ChemStitch rather than redrawing from scratch.

Step 1: Export from ChemDraw as CDXML

In ChemDraw, go to File > Save As and choose CDXML as the format. CDXML is ChemDraw's XML-based file format that preserves structural information.

If your file is already in .cdxml format, you're ready to import. If it's in .cdx (binary ChemDraw format), open it in ChemDraw first and re-save as .cdxml.

Step 2: Import into ChemStitch

In ChemStitch, drag the .cdxml file onto the browser window, or use the import dialog (Ctrl+O). ChemStitch auto-detects the CDXML format from the file extension or content — you don't need to select a format manually.

The structure loads onto the canvas immediately.

Step 3: Understand the stereochemistry warning

When you import a CDXML file, ChemStitch displays a warning: "Some ChemDraw-specific display properties may render differently." This is a transparency measure, not an error.

What it means: ChemDraw stores display-layer metadata (custom colors, label positions, arrow styles) that are specific to ChemDraw's rendering engine. ChemStitch imports the chemical structure faithfully, but some purely cosmetic properties may look different.

The molecular identity — atoms, bonds, stereochemistry — is preserved. If your structure has stereocenters defined in the CDXML, they will import correctly as wedge and dash bonds.

Step 4: Continue working

Once imported, your structure works like any other molecule in ChemStitch. You can edit it, ask the AI about its properties, plan synthetic routes, or export it in other formats (MOL V2000, MOL V3000, SDF, or RXN).

Your imported structure auto-saves to the cloud, so you can close the browser and come back to it later.

Current limitations

ChemStitch supports CDXML import but not CDXML export. If you need to send structures back to a ChemDraw user, export as MOL V2000 — this is the most universally compatible chemical file format and ChemDraw imports it without issues.

ChemStitch does not import .cdx (binary ChemDraw) files. If your files are in .cdx format, open them in ChemDraw and re-save as .cdxml before importing.

Other supported import formats

In addition to CDXML, ChemStitch imports SMILES, MOL V2000, MOL V3000, SDF, InChI, and RXN files. All formats are auto-detected. See the File Formats documentation for the complete reference.