bio-pdb-structure-modification
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.
npx skills add BioTender-max/awesome-bio-agent-skills --skill structure-modification --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
## Version Compatibility Reference examples tested with: BioPython 1.83+, numpy 1.26+ Before using code patterns, verify installed versions match. If versions differ: - Python: `pip show <package>` then `help(module.function)` to check signatures If code throws ImportError, AttributeError, or TypeError, introspect the installed package and adapt the example to match the actual API rather than retrying. # Structure Modification **"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. ## Required Imports ```python from Bio.PDB import PDBParser, PDBIO, StructureBuilder from Bio.PDB.Structure import Structure from Bio.PDB.Model import Model from Bio.PDB.Chain import Chain from Bio.PDB.Residue import Residue from Bio.PDB.Atom import Atom import numpy as np ``` ## Transforming Coordinates ```python from Bio.PDB import PDBParser, PDBIO import numpy as np parser = PDBParser
- Version Compatibility
- Required Imports
- Transforming Coordinates
- Rotation Around Axis
- Applying Transformation Matrix
- Center Structure at Origin
- Removing Atoms
- Removing Residues
- Removing a Chain
- Modifying B-factors
- Modifying Occupancy
- Renumbering Residues
- Changing Chain ID
- Building Structure from Scratch
What does the bio-pdb-structure-modification skill do?
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.
How do I install it?
Run `npx skills add BioTender-max/awesome-bio-agent-skills --skill structure-modification --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From BioTender-max/awesome-bio-agent-skills, a repository with 135 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.