pymol3d — 3D molecular visualization (Streamlit app)

This is a learning / practice project I built to get hands‑on with Streamlit and py3Dmol for interactive molecular visualization, with coding assistance from Cursor (AI pair‑programmer).
The app supports protein, protein–ligand, protein–protein, and ligand visualization using py3Dmol (3Dmol.js) in the browser — no PyMOL desktop installation required.

Layout

• Center (~65%): Interactive 3D viewer (rotate, zoom, pan with mouse).
• Right bar (~35%): PDB load (ID + chain or file upload), chain/ligand selection, protein color & style, ligand color, protein opacity.
• Center tabs: 3D viewer, Hydrogen bonds, 2D interaction plot (PLIP) — PLIP residue–interaction heatmap and PNG export (optional).

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How to use

3D viewer mode

1. Load a structure
   In the right panel under Structure, enter a PDB ID (e.g. 8R4V) or upload a .pdb / .ent file, then click Load structure.

2. Choose chain and ligand
   Use Chain and Ligand in the Chain & ligand section to focus on a specific chain and ligand (or leave as “All” / “None”).

3. Adjust the view
   In Representation you can:

   • Pick a Preset (e.g. PyMOL Publication, Ligand cartoon, Chimera Cartoon) or Custom for manual control.
   • Set Protein color (e.g. by secondary structure, by chain, spectrum, solid).
   • Set Ligand color (element/CPK or theme colors).
   • Set Protein style (cartoon, surface, lines, sticks, trace) and Protein opacity.
   • Change the 3D viewer background (gray, white, black).

4. Analysis and tools
   In Analysis you can enable H-bonds, binding-site focus, and 3D pharmacophore. Under Tools use Residues to focus and Protein sequence. In the viewer area, tabs give 3D viewer, Hydrogen bonds, and 2D interaction plot (PLIP).

5. Viewer — Rotate, zoom, pan with the mouse; use full-screen in the viewer, Escape to exit.

2D viewer mode

Switch Mode to 2D viewer. In the right panel use 2D molecule to look up by name or paste SMILES, then Draw or Load into editor. Use Molecular descriptors and Fingerprints for properties and batch CSV.

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Run the app

From the project root:

pip install -r requirements.txt
streamlit run src/pymol3d_app.py

Optional: ./scripts/run_pymol3d_chrome.sh (opens in Chrome). Notebook: notebooks/pymol3d.ipynb.

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Tips

• 3D: Use Cartoon + By secondary structure for a classic protein view. Use Surface with lower opacity to see the binding pocket around the ligand.
• 2D: ESOL LogS is log10 of molar aqueous solubility. Use download buttons to save PNGs and CSV tables.

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Acknowledgments

This project was developed with coding assistance from Cursor (AI pair-programmer). Cursor is credited here in the documentation; all commits to this repository are authored by the maintainer.