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

Project links

Data verified by PyPI on Aug 4, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

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  • Released:
Latest release

1 maintainer

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Avatar for cewinharhar from gravatar.com cewinharhar

Credits

Author: Omics-OS

GitHub Statistics

Data verified by PyPI on Aug 4, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

AGPL-3.0-or-later
View SPDX License List

Requires

Python <3.14, >=3.12

Tags

bioinformatics protein-structure pymol pdb structural-biology 3d-visualization

Classifiers

Report project as malware

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