A simple but powerful VSCode extension for visualizing protein structures using the Molstar framework, featuring advanced capabilities for sequence alignment, diffusion animations, and confidence scoring.

• Multi-Format Support: Load and visualize molecular structures from PDB, mmCIF, PDBQT, GRO, XYZ, MOL, MOL2, and SDF files
• Interactive 3D Viewer: Powered by Molstar for high-performance molecular visualization
• Multiple Color Schemes: Custom colors, element-based, residue-based, and chain-based coloring
• Grid View: Display multiple structures simultaneously in a grid layout

• Sequence Loading: Load entire folders of structure files as diffusion sequences
• Animation Controls: Play, pause, step through frames with speed control
• Download Animations: Export animations as video files or frame sequences

• FASTA Support: Load and parse FASTA sequence files
• ESMFold Integration: Fold protein sequences using ESMFold API
• Dual Session Mode: Compare original and predicted structures side-by-side
• pLDDT Confidence Coloring: Visualize prediction confidence with color coding
• Alignment Tools: Manual alignment mode with RMSD calculation

• Cartoon Representation: Optimized cartoon rendering for clear structural visualization
• Confidence Coloring: pLDDT confidence scores with color legend
• Interactive Controls: Collapsible panels, zoom, rotate, translate
• Multiple Layout Modes: Single view, dual session, grid view

1. Open VSCode
2. Go to Extensions (Ctrl+Shift+X / Cmd+Shift+X)
3. Search for "Nano Protein Viewer"
4. Click Install

1. Open Command Palette: Ctrl+Shift+P (Windows/Linux) or Cmd+Shift+P (Mac)
2. Run Command: Type "Nano Protein Viewer" and select "Open Nano Protein Viewer"
3. Load Files: Use the VSCode integration buttons to load structure files, folders, or FASTA sequences

• Right-click structure files: Select "Launch Nano Viewer from file(s)"
• Right-click folders: Select "Load Folder in Nano Viewer" to load as diffusion sequence
• Right-click FASTA files: Select "Load FASTA in Nano Viewer"

• nano-protein-viewer.start: Open the protein viewer
• nano-protein-viewer.loadPDBFiles: Launch Nano Viewer from file(s)
• nano-protein-viewer.loadFolder: Load folder as diffusion sequence
• nano-protein-viewer.loadFASTA: Load FASTA file

1. Single Files: Use "Load Structure Files" button or right-click context menu
2. Multiple Files: Select multiple structure files to load simultaneously
3. Folder Loading: Load entire folders for diffusion sequence animations

1. Enable Sequence Alignment: Toggle the "Seq Alignment" switch in the control panel
2. Load FASTA: Either upload a FASTA file or paste sequences directly
3. Fold Sequences: Use "Fold All with ESMFold" to generate 3D structures
4. Compare Structures: Switch between display modes:
   • Dual Session: Original structure (left) vs predicted (right)
   • Seq Structure Only: Show only predicted structure
   • Align Mode: Both structures in single session for manual alignment

When loading diffusion sequences:

• Play/Pause: Control animation playback
• Step Controls: Navigate frame by frame
• Speed Control: Adjust playback speed (0.1x to 5.0x)
• Direction: Play forward or backward
• Download: Export animations as video files or frame sequences

• Custom: Choose from predefined color palette
• Element: Color by chemical element
• Residue: Color by amino acid residue type
• Chain: Color by protein chain
• pLDDT Confidence: Automatic for predicted structures
  • Blue: Very High confidence (>90)
  • Light Blue: Confident (70-90)
  • Yellow: Low confidence (50-70)
  • Orange: Very Low confidence (<50)

• VSCode 1.62.0 or higher
• Internet connection for Molstar CDN resources
• Optional: Internet connection for ESMFold API

The extension works out of the box with no additional configuration required. All settings are managed through the interactive control panel within the viewer.

• Structure Files: .pdb, .PDB, .cif, .CIF, .mmcif, .MMCIF, .pdbqt, .PDBQT, .gro, .GRO, .xyz, .XYZ, .mol, .MOL, .mol2, .MOL2, .sdf, .SDF
• Sequence Files: .fasta, .FASTA, .fa, .FA, .fas, .FAS

• Arrow Keys: Navigate between loaded files
• Mouse Controls:
  • Left Click + Drag: Rotate structure
  • Right Click + Drag: Translate structure
  • Mouse Wheel: Zoom in/out
  • Shift + Mouse Wheel: Adjust clipping planes

1. Performance: Use grid view for comparing multiple structures efficiently
2. Large Files: The viewer handles large protein complexes well due to Molstar's optimization
3. Sequence Matching: The extension automatically attempts to match sequence names with loaded structure files
4. Confidence Colors: pLDDT coloring is automatically applied to ESMFold predictions
5. Animation Performance: Adjust animation speed for smooth playback on different hardware

1. Viewer Not Loading: Check internet connection for Molstar CDN resources
2. File Format Errors: Ensure files are valid molecular structure format
3. ESMFold Errors: Check sequence length (10-1000 amino acids) and internet connection
4. Performance Issues: Close unused grid viewers or reduce animation speed

• "Invalid structure file": File format is not recognized or corrupted
• "No valid structures found": No structure files in selected folder
• "ESMFold API error": Network issue or invalid sequence
• "Sequence too short/long": ESMFold requires 10-1000 amino acids

This extension is based on the Molstar framework. For issues or feature requests, please check the repository or create an issue.

MIT License - see LICENSE file for details.

If you use this extension in your research, please cite the underlying Mol* framework:

@article{sehnal2021molstar,
    author = {Sehnal, David and Bittrich, Sebastian and Deshpande, Mandar and Svobodová, Radka and Berka, Karel and Bazgier, Václav and Velankar, Sameer and Burley, Stephen K and Koča, Jaroslav and Rose, Alexander S},
    title = "{Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures}",
    journal = {Nucleic Acids Research},
    volume = {49},
    number = {W1},
    pages = {W431-W437},
    year = {2021},
    month = {05},
    issn = {0305-1048},
    doi = {10.1093/nar/gkab314},
    url = {https://doi.org/10.1093/nar/gkab314}
}

• Mol Team*: For the excellent molecular visualization framework (see citation above)
• Inspired by: The original protein viewer from molstar/VSCoding-Sequence
• ESMFold/Meta: For the protein folding API
• PDB: For structure data standards
• VSCode Team: For the excellent extension API

• Added support for additional file formats: PDBQT, GRO, XYZ, MOL, MOL2, SDF
• Minor UI updates

• Enhanced start command with input box for PDB/AFDB ID
• Added download icon to download all files as ZIP functionality
• Minor UI updates

• Updated README.md

• Initial release
• Basic structure viewing with Molstar
• Sequence alignment and ESMFold integration
• Diffusion animation support
• Grid view and dual session modes
• pLDDT confidence coloring
• VSCode integration with context menus

Enjoy exploring protein structures with the Nano Protein Viewer! 🧬✨# nano-protein-viewer