Add 2D chemical structures to your illustrations with ChemRender

With ChemRender Beta, you can generate accurate 2D chemical structures directly in BioRender using either a molecule name or a SMILES string (a common chemistry format). You can then fine-tune the look (like atom colors and line thickness), plus resize, rotate, and adjust transparency.

Ways to add a molecule

You can import a molecule in two ways:

1. Search by molecule name (best for common, known compounds)
2. Paste a SMILES string (best for novel or non-public compounds)

💡 Tip: For reaction schemes, import each reactant/product molecule individually, then build the scheme in BioRender using arrows and labels.

1. Importing by molecule name

BioRender searches for named molecules in NIH’s PubChem repository.

Steps to import by name:

1. Open BioRender Editor
   • Select ChemRender from the side panel.
2. Search by name
   • Type a common name (for best results) or other synonym.
3. Visually inspect the matched molecule
   • Check the corresponding 2D structure and the matched name that appears below.
4. Add to the canvas
   • Translate, resize and rotate the molecule to fit your illustration
5. Use the edit panel to adjust style
   • Adjust styling like atom colors, thickness (bold/heavy lines), and transparency

💡 Tip: If your first search doesn’t work, try another common synonym. Some identifiers (like CAS numbers or manufacturer IDs) can work, but are not as reliable as more common names.

2. Importing by SMILES

SMILES is a common chemistry format and encodes a molecule’s structure in a text string (for example, aspirin’s SMILES string is : CC(=O)OC1=CC=CC=C1C(=O)O).

Steps to import by SMILES:

1. Open BioRender Editor
   • Select ChemRender from the side panel.
2. Render your SMILES string
   • Paste in your SMILES string.
3. Visually inspect the resulting molecule
   • Check the corresponding 2D structure
   • Note: Structures from SMILES will not have a name associated with it.
4. Add to the canvas
   • Translate, resize and rotate the molecule to fit your illustration
5. Use the edit panel to adjust style
   • Adjust styling like atom colors, thickness (bold/heavy lines), and transparency

💡 Tip: If you’re importing with SMILES, make sure stereochemistry is included in the string (for example using @ / @@). If it’s missing, the imported structure won’t specify stereochemistry.

Frequently asked questions

What file formats does ‘ChemRender’ support?

Currently, a molecule’s name and SMILES are supported.

Does ‘ChemRender’ support stereochemistry?

ChemRender supports stereochemistry. If you add a molecule by its name, it will visualize the known stereochemistry in the retrieved structure. If you import by SMILES, stereochemistry must be encoded in the SMILES; otherwise it won’t be specified.

Can ‘ChemRender’ support reaction schemes?

Full reaction scheme import isn’t supported, but you can import the individual small molecules and build schemes using BioRender arrows/textboxes.

How do I get a SMILES string?

• Export/copy SMILES from tools like ChemDraw or ChemSketch.
• Many computational chemistry workflows output SMILES.
• You can also look up examples on PubChem by searching a molecule of interest

Why does my molecule look different?

A SMILES string doesn’t include 2D coordinates, so the chemical structure is generated algorithmically. As a result, the same SMILES can generate structures that look different across tools while maintaining the exact same information. Also, related molecules may render with different orientations.

What kinds of molecules can I import?

• Best suited for single small molecules.
• Complex ring systems/stereocenters can produce artifacts in automated 2D rendering.
• Multi-component molecules may work, but results aren’t guaranteed (e.g., multiple APIs/salts).
• Large macromolecules (peptides/DNA/RNA) can be encoded in SMILES, but 2D structures aren’t the preferred representation (other formats like HELM are better suited).

Can ‘ChemRender’ support ChemDraw files?

Not at this time - proprietary formats like ChemDraw .cdx aren’t supported. You will need to export from ChemDraw (or similar) as SMILES, then use that to draw your novel molecule. Or you can use a molecule’s name if available.

How does ‘ChemRender’ compare to ChemDraw?

ChemRender focuses on generating an accurate 2D structure from SMILES with limited styling edits; it does not support full atom-level editing and other features available on ChemDraw. We see ChemRender as a first step to building additional tools to help visualize chemistry.

Need help or have feedback?

1. Email: support@biorender.com
2. Live Chat: Available by clicking on the "Help" bubble in the web app on the bottom right-hand corner.