Biopython Bioinformatics
aiming-lab/AutoResearchClaw
Quick reference for Biopython work: sequence operations, SeqIO file parsing, BLAST searches, Entrez queries, phylogenetic trees and PDB structure analysis.
Agent skill
Bio Pdb Structure Modification
by FreedomIntelligence in FreedomIntelligence/OpenClaw-Medical-Skills
Modify protein structures using Biopython Bio.PDB. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
Install Bio Pdb Structure Modification
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a claude-codeProject install by default; add -g for ~/.claude/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-modification --agent claude-codeProject scope by default; add --scope user for a personal install. Needs GitHub CLI 2.90.0 or later (public preview).
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .claude/skills && cp -r skills-src/skills/bio-pdb-structure-modification .claude/skills/bio-pdb-structure-modification && rm -rf skills-srcUse ~/.claude/skills/ instead of .claude/skills for a personal install. The folder must contain SKILL.md.
Claude Code skills documentation · loads skills from .claude/skills/
Install the "bio-pdb-structure-modification" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modification into .claude/skills/bio-pdb-structure-modification/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-modification", then confirm the skill loads.Claude Code copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$skill-installer install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modificationType this inside Codex. $skill-installer <name> installs a curated skill from openai/skills. The installer writes to $CODEX_HOME/skills (default ~/.codex/skills). Restart Codex if the skill does not show up.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a codexProject install goes to .agents/skills/; add -g for ~/.codex/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-modification --agent codexProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .agents/skills && cp -r skills-src/skills/bio-pdb-structure-modification .agents/skills/bio-pdb-structure-modification && rm -rf skills-srcUse ~/.agents/skills/ instead of .agents/skills for a personal install.
Codex skills documentation · loads skills from .agents/skills/
Install the "bio-pdb-structure-modification" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modification into .agents/skills/bio-pdb-structure-modification/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-modification", then confirm the skill loads.Codex copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a cursorProject install goes to .agents/skills/; add -g for ~/.cursor/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-modification --agent cursorProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .cursor/skills && cp -r skills-src/skills/bio-pdb-structure-modification .cursor/skills/bio-pdb-structure-modification && rm -rf skills-srcUse ~/.cursor/skills/ instead of .cursor/skills for a personal install.
Cursor skills documentation · loads skills from .cursor/skills/, .agents/skills/, .claude/skills/, .codex/skills/
Install the "bio-pdb-structure-modification" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modification into .cursor/skills/bio-pdb-structure-modification/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-modification", then confirm the skill loads.Cursor copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gemini skills install https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git --path skills/bio-pdb-structure-modification--scope user (default) or --scope workspace; --path is the subfolder of the repo that holds the skill; --consent skips the security confirmation prompt.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a gemini-cliProject install goes to .agents/skills/; add -g for ~/.gemini/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-modification --agent gemini-cliProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .gemini/skills && cp -r skills-src/skills/bio-pdb-structure-modification .gemini/skills/bio-pdb-structure-modification && rm -rf skills-srcUse ~/.gemini/skills/ instead of .gemini/skills for a personal install, then run /skills reload.
Gemini CLI skills documentation · loads skills from .gemini/skills/, .agents/skills/
Install the "bio-pdb-structure-modification" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modification into .gemini/skills/bio-pdb-structure-modification/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-modification", then confirm the skill loads.Gemini CLI copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-modificationInstalls for Copilot at project scope by default; add --scope user for a personal install. Preview a skill first with gh skill preview. Needs GitHub CLI 2.90.0 or later (public preview).
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a github-copilotProject install goes to .agents/skills/; add -g for ~/.copilot/skills/.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .github/skills && cp -r skills-src/skills/bio-pdb-structure-modification .github/skills/bio-pdb-structure-modification && rm -rf skills-srcUse ~/.copilot/skills/ instead of .github/skills for a personal install. Commit .github/skills so cloud agent and code review can use it.
GitHub Copilot skills documentation · loads skills from .github/skills/, .claude/skills/, .agents/skills/
Install the "bio-pdb-structure-modification" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modification into .github/skills/bio-pdb-structure-modification/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-modification", then confirm the skill loads.GitHub Copilot copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
$ npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a opencodeOpenCode documents no install command of its own. Project install goes to .agents/skills/; add -g for ~/.config/opencode/skills/.
$ gh skill install FreedomIntelligence/OpenClaw-Medical-Skills bio-pdb-structure-modification --agent opencodeProject scope by default (.agents/skills/); add --scope user for a personal install.
$ git clone --depth 1 https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills.git skills-src && mkdir -p .opencode/skills && cp -r skills-src/skills/bio-pdb-structure-modification .opencode/skills/bio-pdb-structure-modification && rm -rf skills-srcUse ~/.config/opencode/skills/ instead of .opencode/skills for a personal install.
OpenCode skills documentation · loads skills from .opencode/skills/, .claude/skills/, .agents/skills/
Install the "bio-pdb-structure-modification" agent skill from https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-pdb-structure-modification into .opencode/skills/bio-pdb-structure-modification/ in this project. Copy the whole folder (SKILL.md and every file beside it), keep the folder name "bio-pdb-structure-modification", then confirm the skill loads.OpenCode copies the folder itself, the same result as the manual copy. Check what it changed before you commit it.
Facts
- Skill name
bio-pdb-structure-modification- GitHub stars
- 3.1k
- Used in
- 1 other repo
- Token cost
- ~2.8k tokens
- SKILL.md length
- 173 words
- Files
- 5
- Skills in repo
- 173
- Repo updated
- First seen
- Licence
- None found
At a glance
Modify protein structures using Biopython Bio.PDB. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.
- Transforming coordinates
- SKILL.md covers Version Compatibility, Required Imports, Transforming Coordinates and Rotation Around Axis, plus 16 more sections
- Runs Python scripts from its folder; calls pip
- Adding new entities
What it does
Bio Pdb Structure Modification is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. 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.
Its SKILL.md is about 2.8k tokens, which your agent loads only when the skill is triggered. The skill folder holds 5 other files (for example `examples/modify_bfactor.py`, `examples/remove_water.py` and `examples/transform_coords.py`).
It sits in Research & Science, covering Bioinformatics and Protein structure and design. It works with Biopython. The repository describes itself as: The largest open-source medical AI skills library for OpenClaw🦞.
When your agent uses it
- Transforming coordinates
- Adding new entities
- Modifying B-factors and occupancies
- Building structures programmatically
Example prompts
- “/bio-pdb-structure-modification”
Requirements
- Python 3
What it can do on your machine
Read from SKILL.md and the folder at commit b1f9b6e. It shows what the files ask for, not the result of running them.
Tool permissions
Pre-approves nothing: there is no allowed-tools line, so your agent's usual permission prompts apply.
From allowed-tools in the SKILL.md frontmatter.
Runs code
Ships script files (Python), which the agent can run.
Shell commands in SKILL.md call:
pip
From the folder's file list and the shell code blocks in SKILL.md.
Network
No URLs in SKILL.md. Its commands use pip, which can reach the network depending on how they are called.
From URLs in SKILL.md, links to its own repository left out.
Credentials
Names no API keys, tokens, secrets or passwords.
From names ending in _API_KEY, _TOKEN, _SECRET, _KEY or _PASSWORD in SKILL.md.
Context cost
Bio Pdb Structure Modification loads about 2.8k tokens when it runs. Until then it costs about 61 tokens; SKILL.md has 173 words of instructions outside code blocks.
Estimates: characters ÷ 4, the usual rule of thumb; real counts depend on the model's tokenizer. Scripts and assets cost tokens only if the agent reads them.
Safety
Auto-check passed
The automated check found no risky patterns in SKILL.md.
Automated static check — not a guarantee. Review scripts before installing. It scans the text of SKILL.md for risky patterns (piping downloads into a shell, reading credential files, hidden Unicode, destructive commands); files beside SKILL.md are not scanned.
SKILL.md
Without a licence we can't republish the file, so here is its outline and opening line. It has 173 words (~2,782 tokens).
“Reference examples tested with: BioPython 1.83+, numpy 1.26+”
- name
- bio-pdb-structure-modification
- tool_type
- python
- primary_tool
- Bio.PDB
Files
SKILL.md and 4 other files in skills/bio-pdb-structure-modification of FreedomIntelligence/OpenClaw-Medical-Skills.
- SKILL.md
- examples/modify_bfactor.py
- examples/remove_water.py
- examples/transform_coords.py
- usage-guide.md
Open the folder on GitHubat commit b1f9b6e
Used in 1 other repository
We found 1 copy of this SKILL.md (exact, near-identical or edited) in other folders, from 1 other GitHub owner. This page covers the copy in FreedomIntelligence/OpenClaw-Medical-Skills, which our catalogue first saw on October 7, 2026.
Compare with similar skills
Bio Pdb Structure Modification next to the 5 skills that share the most tags, products or categories with it. Stars are the repository's; “used in” counts other GitHub owners with a copy.
| Skill | Stars | Used in | Tokens | Auto-check | Licence | Repo updated |
|---|---|---|---|---|---|---|
| Bio Pdb Structure Modification this skillFreedomIntelligence/OpenClaw-Medical-Skills | 3.1k | 1 repos | ~2.8k | Automated safety check: Pass | None | |
| Biopython Bioinformaticsaiming-lab/AutoResearchClaw | 15k | — | ~810 | Automated safety check: Pass | MIT | |
| Ggetdavila7/claude-code-templates | 32k | 11 repos | ~6.3k | Automated safety check: Pass | MIT | |
| Bio Entrez LinkGPTomics/bioSkills | 1.2k | 2 repos | ~3.8k | Automated safety check: Pass | MIT | |
| Bio Structural Biology Geometric AnalysisGPTomics/bioSkills | 1.2k | 1 repos | ~4.9k | Automated safety check: Pass | MIT | |
| Bio Structural Biology Structure IoGPTomics/bioSkills | 1.2k | 1 repos | ~4k | Automated safety check: Pass | MIT |
Similar skills
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davila7/claude-code-templates
CLI/Python toolkit for rapid bioinformatics queries. An agent skill from davila7/claude-code-templates.
Bio Entrez Link
GPTomics/bioSkills
Find cross-database references between NCBI databases using Biopython Bio.Entrez (ELink).
Bio Structural Biology Geometric Analysis
GPTomics/bioSkills
Measures geometric properties of protein structures with Biopython Bio.PDB - interatomic distances, distance matrices, bond and dihedral angles (phi/psi/chi, Ramachandran), superposition and RMSD…
Bio Structural Biology Structure Io
GPTomics/bioSkills
Reads, writes, downloads, and converts macromolecular structures with Biopython Bio.PDB.
Bio Structural Biology Structure Modification
GPTomics/bioSkills
Modifies protein structures in place with Biopython Bio.PDB - transforms coordinates, strips waters/heteroatoms, overloads the B-factor column, renumbers, and builds entities.
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Related
Works with
Categories
Questions about Bio Pdb Structure Modification
What does Bio Pdb Structure Modification do?
Modify protein structures using Biopython Bio.PDB. An agent skill from FreedomIntelligence/OpenClaw-Medical-Skills. Bio Pdb Structure Modification is an agent skill from FreedomIntelligence/OpenClaw-Medical-Skills.PDB.
When should I use Bio Pdb Structure Modification?
Bio Pdb Structure Modification fits situations like: transforming coordinates; adding new entities; modifying B-factors and occupancies; building structures programmatically.
How do I install Bio Pdb Structure Modification in Claude Code?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a claude-code`. Or copy the skill folder (skills/bio-pdb-structure-modification in FreedomIntelligence/OpenClaw-Medical-Skills) into .claude/skills/bio-pdb-structure-modification in your project. Claude Code loads it when a task matches its description.
How do I install Bio Pdb Structure Modification in Codex?
Run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a codex`. Or copy the skill folder (skills/bio-pdb-structure-modification in FreedomIntelligence/OpenClaw-Medical-Skills) into .agents/skills/bio-pdb-structure-modification in your project. Codex loads it when a task matches its description.
Can I use Bio Pdb Structure Modification in Cursor, Gemini CLI or GitHub Copilot?
Cursor, Gemini CLI, GitHub Copilot and OpenCode also load SKILL.md folders. With the skills CLI, run `npx skills add FreedomIntelligence/OpenClaw-Medical-Skills --skill bio-pdb-structure-modification -a cursor` (or -a gemini-cli, github-copilot or opencode for the others). To copy it by hand, put the folder in .cursor/skills/bio-pdb-structure-modification, .gemini/skills/bio-pdb-structure-modification, .github/skills/bio-pdb-structure-modification and .opencode/skills/bio-pdb-structure-modification in your project.
What does Bio Pdb Structure Modification need to run?
Going by SKILL.md and its folder, Bio Pdb Structure Modification needs Python for the scripts in its folder and the command-line tools its instructions call (pip). Our summary lists: Python 3.
Does Bio Pdb Structure Modification access the network?
SKILL.md contains no URLs. Its commands use pip, which can reach the network depending on how they are called. This is read from the text; nothing was executed.
Is Bio Pdb Structure Modification safe to install?
Our automated static check of SKILL.md found no risky patterns, such as piping downloads into a shell, reading credential files or hidden Unicode. It is not a guarantee. Review the folder before installing.
What licence does Bio Pdb Structure Modification use?
No licence was found for Bio Pdb Structure Modification or its repository. Without one, default copyright applies: ask the author before reusing or redistributing it.
How many tokens does Bio Pdb Structure Modification use?
About 2.8k tokens (SKILL.md is roughly 11k characters). Agents keep only the skill's name and description in context until a task matches; then they load SKILL.md in full.
What are the alternatives to Bio Pdb Structure Modification?
Skills that share tags, products or a category with Bio Pdb Structure Modification: Biopython Bioinformatics (aiming-lab/AutoResearchClaw, 15k stars), Gget (davila7/claude-code-templates, 32k stars), Bio Entrez Link (GPTomics/bioSkills, 1.2k stars) and Bio Structural Biology Geometric Analysis (GPTomics/bioSkills, 1.2k stars). The comparison table on this page puts their stars, adoption, token cost, safety result and licence side by side.
Who maintains Bio Pdb Structure Modification?
FreedomIntelligence (a GitHub organization) maintains it in FreedomIntelligence/OpenClaw-Medical-Skills, which has 3,051 GitHub stars. The repository holds 173 skills in this directory. The repository was last updated on July 21, 2026.
Source: FreedomIntelligence/OpenClaw-Medical-Skills on GitHub. Facts on this page come from the repository at the commit we read; the author's words are quoted as theirs.