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Mol Star Viewer

VERIFIED

## Connections

visualization protein-structure

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

1. Open https://molstar.org/viewer/

2. Drag & drop PDB/mmCIF file

3. 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)

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)