ChemRender3D

Bring interactive 3D molecules to Obsidian.

ChemRender3D brings the Mol* molecular viewer directly into your vault. Visualize and explore proteins, crystal structures, atoms and small molecules without leaving your notes.

Features

• Native embeds — Render .pdb, .cif, .mol, .sdf, .xyz, and other supported molecular files.
• Mol* sessions — Embed a .molx or .molj session and get back exactly the scene you saved.
• 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.
• Sized embeds — Set a viewer's width and height with Obsidian's |WIDTHxHEIGHT suffix.
• Molecular orbitals — Show the HOMO, LUMO or any other orbital of a small molecule, computed right in your note, or load real quantum-chemistry results from .molden files.

📝 Release Notes

⚡ (1.0.6)

• Molecular orbitals for any small molecule — A new orbital button computes the molecular orbitals in the note with Extended Hückel theory, the classic qualitative MO method from organic-chemistry teaching. No files or external software needed.
• MO energy diagram — Occupied levels with ↑↓ electrons, HOMO/LUMO and the gap, and which atoms each orbital lives on. Click a level to draw it in its two phases (blue/red), show the total electron density (ρ), or resize the lobes.
• .molden support — Embed orbitals from xtb, ORCA, PySCF or Psi4 calculations.
• New 3dmol options — orbital:, iso: and charge:.
• Fixes — The Show UI panels setting is now respected, so Mol*'s side panels stay hidden by default. Also fixed: XYZ files with a blank comment line lost their first atom; SMILES lookups now use PubChem's SMILES endpoint; MOL/SDF files with 100+ atoms or bonds now parse; formal charges are read from SDF files; inline styles on 2D cards and grids are now applied.

⚡ (1.0.5)

• Mol* sessions — Embed a .molx or .molj session and get back exactly the scene you saved. (Thanks @lkndl!)
• Sized embeds — Set a viewer's width and height with Obsidian's |WIDTHxHEIGHT suffix. (Thanks @lkndl!)

molx/embeds demo:

⚡ (1.0.4)

• Extended Chemical & Material Formats.

• 2D Structure Mode: Toggle between responsive 3D viewports and textbook 2D vector diagrams.

• Fast 2D Collection Grid: Folder previews now generate instant vector cards.

• Click-to-3D Focus Modal: Click any molecule in the grid gallery to launch a dedicated 3D inspection window.

• Use ```2dmol for any individual molecule, crystal, file, or SMILES:

  ```2dmol
  c1ccccc1
  ```
  

  ```2dmol
  [[m-Xylene_.mol]]
  ```
  

  ```2dmol
  caffeine
  ```
  

  

2dmol demo:

🗂️ 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.

Set the viewer size

Use Obsidian's usual embed size suffix, in pixels:

![[hemoglobin.pdb|200x500]]   <!-- 200 px wide, 500 px high -->

![[hemoglobin.pdb|300]]       <!-- 300 px wide, default height -->

As with images, a width on its own leaves the height alone — the viewer keeps the Viewer Height from the plugin settings. The same suffix works inside 3dmol, 2dmol and file: links:

```3dmol
[[aspirin.mol|640x480]]
```

Embed a saved Mol* session

A session saved from the Mol* viewer (State → Download in Mol*, or the Save State control) can be dropped into the vault and embedded like any other structure file:

![[binding-site.molx]]

The session restores its own structures, representations, colour themes, background and camera, so the viewer reproduces the scene as it was saved rather than applying the plugin's default preset. Both the zipped .molx and the plain-JSON .molj form work.

If the session contains more than one snapshot, ‹ 1/4 › buttons appear in the viewer toolbar for stepping through them.

Sessions are 3D only — they carry no flat atom list, so 2dmol and 2d-grid skip them.

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]]
```

Show molecular orbitals

Every small-molecule viewer has an orbital button (the two-lobe icon in the toolbar). Click it to compute the orbitals and open the energy-level diagram. Click any level to draw that orbital; ▲ ▼ step through them, ρ shows the total electron density, and Size changes the contour.

To open a viewer straight on an orbital, add orbital: to a 3dmol block:

```3dmol
pubchem: ibuprofen
orbital: HOMO
```

```3dmol
smiles: C=CC=CC=C
orbital: LUMO
iso: 0.8
```

The orbitals come from Extended Hückel theory, a qualitative method. Orbital shapes, nodes and HOMO/LUMO character are reliable for ordinary organic molecules, which is what you need for teaching. Energies are approximate, and levels that are close in energy can come out in a different order than in a full quantum calculation. Supported elements: H, B, C, N, O, F, Si, P, S, Cl, Br, I. Structures need explicit hydrogens; PubChem and SMILES lookups already include them.

Embed orbitals from a quantum-chemistry calculation

For real computed orbitals, embed a Molden file:

![[water.molden]]

or use file: [[water.molden]] together with orbital: in a 3dmol block. The orbital panel opens automatically and shows your calculation's orbitals and energies. Most programs can write a Molden file:

Spherical s–g functions and Cartesian d functions are supported. For Cartesian f or g functions, ask the program for spherical output.

Settings

• Max Pixel Ratio — Reduce this value on high-resolution displays to improve rendering performance.
• Auto-Spin — Automatically rotate embedded structures.
• Show orbital button — Add the orbital button to small-molecule viewers.
• Orbital surface style — Translucent glow (like the Mol* demo) or solid textbook lobes.
• Default orbital isovalue — Default lobe size; override it per block with iso:.

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.