Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx skills add openscientist-io/openscientist --skill phenix-tools-referencegit clone --depth 1 https://github.com/openscientist-io/openscientistWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/openscientist-io/openscientist/phenix-tools-reference)<a href="https://agentmods.dev/skills/openscientist-io/openscientist/phenix-tools-reference"><img src="https://agentmods.dev/badge/skills/openscientist-io/openscientist/phenix-tools-reference/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/openscientist-io/openscientist/phenix-tools-reference"><img src="https://agentmods.dev/badge/skills/openscientist-io/openscientist/phenix-tools-reference.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5.1 | $0.00015 | $0.02238 |
| Opus 5.5 | $0.00006 | $0.00895 |
| Sonnet 5.5 | $0.00003 | $0.00448 |
| Haiku 4.5 | $0.00002 | $0.00224 |
Grade A, and why
phenix-tools-reference scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2mo ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 195 lines — stays where its author put it; the contents beside it link to each section on GitHub.
Phenix Tools Reference
If Phenix is available, prefer run_phenix_tool over execute_code for structural biology tasks like validation, superposition, refinement, and map analysis. Phenix is the gold standard for these tasks.
Call run_phenix_tool(tool_name="phenix.<command>", input_files=["file.pdb"], description="..."). This reference lists the most useful commands grouped by task. Most commands accept PDB or mmCIF files, but some take map files, reflection data, sequences, or other formats — check each tool's --help if you are unsure.
Validation and Quality Assessment
| Command | Purpose |
|---|---|
phenix.molprobity |
Comprehensive validation: Ramachandran, rotamers, clashes, C-beta deviations; the single best overall quality check |
phenix.clashscore |
All-atom steric clash analysis |
phenix.ramalyze |
Ramachandran backbone analysis |
phenix.rotalyze |
Side-chain rotamer analysis |
phenix.cablam |
C-alpha based backbone validation |
phenix.cbetadev |
C-beta deviation analysis |
phenix.omegalyze |
Cis/trans peptide bond validation |
phenix.model_vs_data |
Model versus diffraction data statistics |
phenix.model_statistics |
Summary geometry statistics for a model |
phenix.emringer |
Map-model validation for cryo-EM structures |
phenix.validation_cryoem |
Comprehensive cryo-EM validation |
phenix.undowser_validation |
Check waters for clashes and poor contacts |
phenix.clashscore2 |
Updated all-atom clash score (prefer over clashscore when available; slightly different scoring) |
phenix.undowser2_validation |
Updated water validation (same relationship to undowser_validation as above) |
phenix.holton_geometry_validation |
Holton-method geometry validation — complementary signal to molprobity; useful for second-opinion checks |
Example: Full validation
run_phenix_tool(
tool_name="phenix.molprobity",
input_files=["structure.pdb"],
description="Comprehensive structure quality check",
)
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2mo ago First seen · 195 lines · 15 tokens per session scan A 5015ecb6cd5d
phenix-tools-reference is a skill published in the GitHub repository openscientist-io/openscientist (63 stars, last pushed yesterday), licensed Apache-2.0. It adds 15 tokens to every session and 2,238 once invoked, about $0.0001 per session on Opus 5.5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-30.
phenix-tools-reference compared with skills from other repositories
| Mod | Type | Stars | Last push | Licence | Scan | Tokens | Works with |
|---|---|---|---|---|---|---|---|
| phenix-tools-referenceopenscientist-io/openscientist | Skill | 63 | yesterday | Apache-2.0 | A | 15 | Claude Code, Codex |
| featool-multiphysicsmahmoud20138/Tradecraft | Skill | 17 | 6mo ago | MIT | A | 66 | Claude Code |
| designerorkait/hyperstack | Skill | 1 | 1mo ago | none | A | 62 | Claude Code |
| instrument-data-to-allotropeanthropics/knowledge-work-plugins | Skill | 35k | 2d ago | Apache-2.0 | A | 123 | Claude Code |
| exploratory-data-analysisK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 83 | Claude Code |
| matlabK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 44 | Claude Code |
| phylogeneticsK-Dense-AI/scientific-agent-skills | Skill | 56k | 4d ago | MIT | A | 71 | Claude Code, Codex |