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bio-pdb-structure-modification

Maintainer FreedomIntelligence · Last updated April 1, 2026

Modify protein structures using Biopython Bio.PDB. Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.

OpenClawNanoClawAnalysisReproductionbio-pdb-structure-modification🧬 bioinformatics (gptomics bio-* suite)bioinformatics — structural biology & cheminformaticsmodify

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modification

Maintainer: FreedomIntelligence
License: MIT
Last updated: April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

Python: Bio.PDB.PDBIO() with Select subclass for filtering, Bio.PDB.Superimposer() for transforms.
Extract a chain from a PDB file" → Remove/add atoms, residues, or chains; transform coordinates; modify B-factors and occupancies; build structures programmatically. Python: Bio.PDB.PDBIO() with Select subclass for filtering, Bio.PDB.Superimposer() for transforms.
Transform coordinates, remove/add entities, modify properties, and build structures programmatically.
translation = np.array([10.0, 0.0, 0.0]) for atom in structure.get_atoms(): atom.coord = atom.coord + translation.

Source Doc

Excerpt From SKILL.md

Transforming Coordinates

from Bio.PDB import PDBParser, PDBIO
import numpy as np

parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')

## Save transformed structure

io = PDBIO()
io.set_structure(structure)
io.save('translated.pdb')

Rotation Around Axis

from Bio.PDB import PDBParser
from Bio.PDB.vectors import rotaxis
import numpy as np

parser = PDBParser(QUIET=True)
structure = parser.get_structure('protein', 'protein.pdb')

Use cases

Use when transforming coordinates, removing atoms or residues, adding new entities, modifying B-factors and occupancies, or building structures programmatically.