Mol* (Molstar) Viewer
Open-source 3D molecular visualization tool. Used by PDB, AlphaFold DB, and many bioinformatics platforms. Runs in browser.
What It Does
- Interactive 3D protein structure visualization
- Color by: chain, pLDDT confidence, secondary structure, residue properties
- Measure distances, angles between atoms
- Superpose multiple structures
- Export images and animations
How to Use
Web (Embedded)
- Already integrated in AlphaFold DB pages
- PDB: https://www.rcsb.org → any structure page
- Standalone: https://molstar.org/viewer/
Load Custom Structure
- Open https://molstar.org/viewer/
- Drag & drop PDB/mmCIF file
- Or paste PDB ID / URL
Useful Operations for STRC
- Color by pLDDT to see confident vs uncertain regions
- Select residue 1659 → show neighborhood → color by charge
- Superpose WT and E1659A structures to see differences
- Measure distance from E1659 to nearest binding partner
Verified Status
VERIFIED — works in browser, STRC structures load and render correctly.
STRC Research Usage
- STRC Protein Visualization — primary visualization tool
- Embedded in AlphaFold DB when viewing Q7RTU9
- Used to inspect E1659A → loss of negative charge visible
Next Steps
- Animation export — create rotating structure GIFs for Shu team / publications
- Electrostatic surface — visualize charge loss at E1659A (Glu→Ala = -1 charge removed)
- Superposition — overlay WT vs E1659A AF3 structures
- Electrostatic analysis already done computationally: ΔΔG = 8.62 kcal/mol (see STRC Electrostatic Analysis E1659A)
Connections
- AlphaFold Database [used-in] — embedded viewer
- PyMOL [see-also] — desktop alternative
- STRC Protein Visualization [used-in]
- STRC Electrostatic Analysis E1659A [see-also]