Bring interactive 3D molecules to Obsidian.
ChemRender3D brings the Mol* molecular viewer directly into your vault. Visualize and explore proteins, crystal structures, and small molecules without leaving your notes.
- Native embeds — Render
.pdb,.cif,.mol,.sdf,.xyz, and other supported molecular files. - SMILES to 3D — Generate and visualize 3D molecular structures directly from SMILES.
- Interactive visualization — Rotate, zoom, and inspect structures inside your notes.
- Multiple representations — Explore structures using molecular, ribbon, surface, and illustrative styles.
- Molecular interactions — Detect hydrogen bonds, salt bridges, and other non-covalent interactions.
- Performance controls — Adjust rendering quality for large molecular structures.
🗂️ New Feature: Folder Grid Preview Want to see all your molecules at a glance? You can now generate a beautiful, responsive gallery of all 3D molecules in a specific folder. Just use this code block:
```3dmol-grid
folder: Assets/Molecules
```example:
Embed a supported file directly in your note:
![[hemoglobin.pdb]]
![[caffeine.sdf]]ChemRender3D automatically replaces the file embed with an interactive 3D viewer.
Use a 3dmol code block:
```3dmol
CC(=O)OC1=CC=CC=C1C(=O)O
```Note: The 3D coordinates from SMILES are generated for visualization and are not intended for geometry optimization or computational analysis.
Alternatively, reference a molecular file inside a 3dmol block:
```3dmol
[[aspirin.mol]]
```- Max Pixel Ratio — Reduce this value on high-resolution displays to improve rendering performance.
- Auto-Spin — Automatically rotate embedded structures.
- Open Settings → Community plugins → Browse.
- Search for ChemRender3D.
- Install and enable the plugin.
ChemRender3D is powered by Mol*, an open-source toolkit for visualization and analysis of large-scale molecular data.