Structural Visualization
Protein structure visualization and analysis agent
In Development — This package is not yet published to PyPI. APIs, tool signatures, and agent behavior will change before release.
lobster-structural-viz
FreeAdvanced
Protein structure visualization: PyMOL, ChimeraX, interaction networks
Input
PDB FilesAlphaFold IDsUniProt IDsStructure URLs
Output
Structure RenderingsInteraction MapsAnalysis ReportsSession Files
Agents (1)
└── protein_structure_visualization_expert — 3D structure visualization and interaction analysis
pip install lobster-structural-viz
Agents
protein_structure_visualization_expert
Specialized agent for protein structure visualization and structural bioinformatics analysis.
Capabilities:
- PDB and AlphaFold structure loading
- PyMOL and ChimeraX rendering
- Protein-protein interaction visualization
- Structure superposition and alignment
- Domain and binding site annotation
Example Workflows
Visualize AlphaFold Structure
User: Load the AlphaFold structure for UniProt ID P12345 and
highlight the active site
[protein_structure_visualization_expert]
- Fetches AlphaFold structure from database
- Loads structure in PyMOL
- Identifies active site residues
- Colors by B-factor (confidence)
- Generates high-resolution rendering
- Saves session fileCompare Protein Structures
User: Superimpose human and mouse versions of protein X and
show the differences
[protein_structure_visualization_expert]
- Loads both PDB structures
- Performs structural alignment (RMSD calculation)
- Superimposes structures
- Highlights divergent regions
- Reports RMSD and alignment statistics
- Generates side-by-side comparison figureProtein Interaction Network
User: Visualize the protein interaction network for these IDs
[protein_structure_visualization_expert]
- Retrieves interaction data (STRING, IntAct)
- Creates network graph
- Maps structures to nodes where available
- Colors by functional annotation
- Exports interaction mapServices
lobster-structural-viz includes structural analysis services bundled with the package:
| Service | Purpose |
|---|---|
| PyMOLService | PyMOL-based structure visualization and rendering |
| ChimeraXService | ChimeraX-based structure visualization |
| StructureAnalysisService | RMSD, alignment, domain annotation |
| ProteinInteractionService | Interaction network visualization |
Services are installed automatically with the agent package.
Dependencies
lobster-structural-viz requires structural bioinformatics tools:
| Library | Purpose |
|---|---|
| pymol | PyMOL Python API (structure visualization) |
| chimerax | ChimeraX Python API (alternative visualizer) |
| BioPython | PDB parsing and structure manipulation |
| networkx | Protein interaction network graphs |
| requests | AlphaFold/PDB database access |
Installation Notes:
- PyMOL:
conda install -c conda-forge pymol-open-source - ChimeraX: Download from UCSF ChimeraX
These dependencies are NOT installed automatically due to platform-specific requirements. Install manually as needed.
Configuration
# .lobster_workspace/config.toml
enabled = ["protein_structure_visualization_expert"]
[protein_structure_visualization_expert]
renderer = "pymol" # or "chimerax"
output_format = "png" # png, ray-traced png, pse (session)
resolution = 1200 # width in pixelsSupported Structure Sources
| Source | ID Format | Access |
|---|---|---|
| PDB | 4HHB, 1ABC | Direct download from RCSB PDB |
| AlphaFold | UniProt ID (P12345) | AlphaFold DB API |
| Local PDB | File path | Load from workspace |
| URL | https://... | Download from custom source |
Rendering Modes
| Mode | Use Case | Output |
|---|---|---|
| Cartoon | Overview, secondary structure | Clean ribbon diagrams |
| Surface | Binding sites, pockets | Molecular surface |
| Sticks | Ligands, active sites | Atomic detail |
| Sphere | Protein complexes | Space-filling |
Visualization Features
Structure Quality Assessment
User: Show the confidence scores for this AlphaFold prediction
[protein_structure_visualization_expert]
- Loads AlphaFold structure with pLDDT scores
- Colors structure by confidence (blue=high, red=low)
- Highlights low-confidence regions
- Reports overall model qualityBinding Site Analysis
User: Identify and visualize potential binding pockets
[protein_structure_visualization_expert]
- Runs pocket detection algorithm
- Highlights surface pockets
- Reports pocket volume and properties
- Suggests druggability scoresIntegration with Proteomics
Structural visualization complements proteomics analysis:
proteomics_expert
-> Identifies differentially abundant proteins
-> Identifies phosphorylation sites
|
v
protein_structure_visualization_expert
-> Maps PTM sites to 3D structure
-> Visualizes spatial distribution
-> Identifies functional domain enrichment