ChemRender3D

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.

Features

• 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:

Usage

Embed molecular files

Embed a supported file directly in your note:

![[hemoglobin.pdb]]

![[caffeine.sdf]]

ChemRender3D automatically replaces the file embed with an interactive 3D viewer.

Generate a structure from SMILES

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.

Reference a file

Alternatively, reference a molecular file inside a 3dmol block:

```3dmol
[[aspirin.mol]]
```

Settings

• Max Pixel Ratio — Reduce this value on high-resolution displays to improve rendering performance.
• Auto-Spin — Automatically rotate embedded structures.

Installation

1. Open Settings → Community plugins → Browse.
2. Search for ChemRender3D.
3. Install and enable the plugin.

Acknowledgment

ChemRender3D is powered by Mol*, an open-source toolkit for visualization and analysis of large-scale molecular data.