lobster-structural-viz
Protein structure visualization and analysis with PyMOL and ChimeraX integration.
Installation
pip install lobster-structural-viz
Agents
| Agent | Description |
|---|---|
protein_structure_visualization_expert |
Structural biology specialist. PDB fetching, 3D visualization, structural analysis, and omics data integration. |
Services
| Service | Purpose |
|---|---|
| ProteinStructureFetchService | Download structures from RCSB PDB with metadata extraction |
| PyMOLVisualizationService | Generate 3D visualizations using PyMOL |
| ChimeraXVisualizationService | Alternative visualizations with UCSF ChimeraX (ALPHA) |
| StructureAnalysisService | Secondary structure, geometry, and RMSD calculations |
Features
Structure Fetching
- Download from RCSB PDB database with automatic caching
- Comprehensive metadata extraction (organism, method, resolution)
- Support for PDB, mmCIF, and biological assembly formats
- Batch download for structure comparison workflows
3D Visualization (PyMOL)
- Interactive mode for GUI-based exploration
- Batch mode for automated PNG image generation
- Multiple representation styles: cartoon, surface, sticks, spheres, ribbon
- Color schemes: chain, secondary_structure, bfactor, element, custom
- Residue highlighting for disease mutations, binding sites, active sites
- Ray-traced high-quality rendering for publication figures
Structural Analysis
- Secondary structure distribution analysis (DSSP)
- Geometric properties: radius of gyration, chain length, surface area
- Residue contact maps and distance matrices
- B-factor analysis for flexibility assessment
Structure Comparison
- RMSD calculation with optional structural alignment
- Biological interpretation of similarity scores
- Chain-specific comparisons for multi-chain complexes
- Sequence identity and structural coverage metrics
Data Integration
- Link gene expression levels to PDB structures
- Filter differentially expressed genes by structure availability
- Cross-reference proteomics data with structural annotations
- Annotate structures with functional data from omics analysis
Requirements
- Python 3.12+
- lobster-ai >= 1.0.0
- PyMOL (optional, for visualization execution)
PyMOL Installation
For visualization execution, install PyMOL:
# macOS/Linux via Homebrew
brew install brewsci/bio/pymol
# Or download from https://pymol.org/
If PyMOL is not installed, the agent generates command scripts that can be executed manually.
Documentation
Full documentation: docs.omics-os.com/docs/agents/structural-viz
License
AGPL-3.0-or-later
1 maintainer
Metadata
1 maintainer
Release files for lobster-structural-viz 1.1.429
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| lobster_structural_viz-1.1.429-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 90.5 kB
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