structure

Bio.PDB provides tools for working with macromolecular 3D structures from PDB and mmCIF files. The module uses the SMCRA (Structure/Model/Chain/Residue/Atom) architecture to represent protein structures hierarchically.

Skills
Scientific
0

What it does and how to use it

A skill that teaches Claude Code to do scientific tasks well. It is packaged knowledge the model uses whenever it is relevant.

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Install (Claude Code)

mkdir -p .claude/skills/structure && curl -fsSL https://doutorai.pt/data/lib/skills__structure.md -o .claude/skills/structure/SKILL.md

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Content

# Structural Bioinformatics with Bio.PDB

## Overview

Bio.PDB provides tools for working with macromolecular 3D structures from PDB and mmCIF files. The module uses the SMCRA (Structure/Model/Chain/Residue/Atom) architecture to represent protein structures hierarchically.

## SMCRA Architecture

The Bio.PDB module organizes structures hierarchically:

```
Structure
  └── Model       (multiple models for NMR structures)
      └── Chain   (e.g., chain A, B, C)
          └── Residue  (amino acids, nucleotides, heteroatoms)
              └── Atom (individual atoms)
```

## Parsing Structure Files

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