lobster-structural-viz

Protein structure visualization and analysis with PyMOL and ChimeraX integration.

Installation

pip install lobster-structural-viz

Agents

Services

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