lobster-structural-viz 1.1.406

Protein structure visualization agent for Lobster AI - 3D structural biology and PyMOL integration

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