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
- Open VSCode
- Go to Extensions (Ctrl+Shift+X / Cmd+Shift+X)
- Search for "Nano Protein Viewer"
- Click Install
- Open Command Palette:
Ctrl+Shift+P(Windows/Linux) orCmd+Shift+P(Mac) - Run Command: Type "Nano Protein Viewer" and select "Open Nano Protein Viewer"
- 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 viewernano-protein-viewer.loadPDBFiles: Launch Nano Viewer from file(s)nano-protein-viewer.loadFolder: Load folder as diffusion sequencenano-protein-viewer.loadFASTA: Load FASTA file
- Single Files: Use "Load Structure Files" button or right-click context menu
- Multiple Files: Select multiple structure files to load simultaneously
- Folder Loading: Load entire folders for diffusion sequence animations
- Enable Sequence Alignment: Toggle the "Seq Alignment" switch in the control panel
- Load FASTA: Either upload a FASTA file or paste sequences directly
- Fold Sequences: Use "Fold All with ESMFold" to generate 3D structures
- 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
- Rainbow: Color by sequence position with multiple palette options
- Classic: Traditional rainbow gradient
- Viridis: Perceptually uniform colormap
- Plasma: High contrast plasma colormap
- Magma: Warm magma colormap
- Blue-Red: Simple blue to red gradient
- Pastel: Soft pastel colors
- 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)
Toggle illustrative rendering for enhanced visual quality:
- Outline Effect: Adds edge outlines to structures for better definition
- Ambient Occlusion: Adds depth perception with shadowing in cavities
- Creates publication-quality visualizations with improved depth and clarity
- 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
- Performance: Use grid view for comparing multiple structures efficiently
- Large Files: The viewer handles large protein complexes well due to Molstar's optimization
- Sequence Matching: The extension automatically attempts to match sequence names with loaded structure files
- Confidence Colors: pLDDT coloring is automatically applied to ESMFold predictions
- Animation Performance: Adjust animation speed for smooth playback on different hardware
- Viewer Not Loading: Check internet connection for Molstar CDN resources
- File Format Errors: Ensure files are valid molecular structure format
- ESMFold Errors: Check sequence length (10-1000 amino acids) and internet connection
- 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 Rainbow Coloring Mode with 6 different color palettes
- Classic rainbow gradient
- Viridis (perceptually uniform)
- Plasma (high contrast)
- Magma (warm tones)
- Blue-Red (simple gradient)
- Pastel (soft colors)
- Added Illustrative Style Rendering
- Outline effect for better structure definition
- Ambient occlusion for enhanced depth perception
- Publication-quality visualization option
- Improved color mode UI with dropdown menu
- Enhanced visual customization options
- 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