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 agentmods add skills/stge4code/shelx-mcp/shelxnpx skills add stge4code/shelx-mcp --skill shelxgit clone --depth 1 https://github.com/stge4code/shelx-mcpWrote 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/stge4code/shelx-mcp/shelx)<a href="https://agentmods.dev/skills/stge4code/shelx-mcp/shelx"><img src="https://agentmods.dev/badge/skills/stge4code/shelx-mcp/shelx.svg" alt="Measured on agentmods" height="20"></a>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 | $0.00042 | $0.00979 |
| Opus 5 | $0.00021 | $0.00490 |
| Sonnet 5 | $0.00008 | $0.00196 |
| Haiku 4.5 | $0.00004 | $0.00098 |
Grade B, and why
shelx scanned grade B with 1 finding 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 6d 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.
Unrestricted tool accessmediumExcessive agency
A wildcard tool grant or "run any command" leaves no least-privilege boundary at all.
- Only the allowlisted programs can run; never try to execute arbitrary commands. How it starts
The opening of the file, as written. The whole thing — 61 lines — stays where its author put it; the contents beside it link to each section on GitHub.
SHELX crystallography workflow
This skill drives the shelx-mcp MCP server, which wraps the SHELX console
programs (SHELXL, SHELXS, SHELXT, SHELXC/D/E, CIFTAB). Use it whenever the user
has crystallographic data (.ins / .hkl) or wants to build/run a SHELX job.
Tools available
list_commands/command_help(name)/search_commands(query)— the bundled, offline SHELXL refinement instruction reference.list_solution_keywords(program)/solution_help(program, keyword)— the bundled SHELXS / SHELXD / SHELXD-MM.inscards (e.g.TREF,FIND,SHEL,DSUL), SHELXT command-line switches (e.g.-a,-d,-L), SHELXC stdin keywords (e.g.SAD,CELL,SPAG) and SHELXE command-line options (e.g.-aN,-h). Programs:shelxs,shelxd,shelxd_mm,shelxt,shelxc,shelxe.validate_ins(ins)— check the required header cards (TITL, CELL, ZERR, LATT, SYMM, SFAC, UNIT, HKLF, END).solve(ins, hkl, program="shelxs")— structure solution (useshelxtfor dual-space/intrinsic phasing).refine(ins, hkl, program="shelxl")— least-squares refinement.run_shelx(program, ins, hkl, ...)— raw runner for any allowed program.analyze_results(lst, res)— extract R1, wR2, GooF (S), max shift/esd, atom count and warnings from SHELXL output.analyze_solution(lxt, res)— extract R1, alpha, space group, Flack x, CC and atom count from SHELXT output (name.lxt+name_a.res).shelx_info()— report the configured SHELX directory and available programs.
Recommended workflow
- Orient. If the user names an unfamiliar instruction, look it up before
writing it:
- refinement card:
command_help("NAME")(orsearch_commandsfor a keyword). - solution keyword:
list_solution_keywords("shelxs")thensolution_help("shelxs", "TREF").
- refinement card:
- Build / receive the model. Get or generate the
.instext, then runvalidate_insand fix any missing header cards. - Solve (if starting from raw data):
solve(ins, hkl). Preferprogram="shelxt"for small molecules (it usually gives a more complete solution than SHELXS); read the returned.lxt/name_a.resand check the outcome withanalyze_solution(lxt=..., res=...)(low R1, sensible space group, Flack x near 0 for the correct absolute structure). - Refine:
refine(ins, hkl). Iterate — tighten restraints, addANIS, adjustWGHT— re-running each time. - Check the outcome:
analyze_results(lst=..., res=...)and react to warnings (e.g. "missed symmetry", non-positive-definite atoms, high R1).
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.
- 6d ago First seen · 61 lines · 42 tokens per session scan B 8eb562cc7034
shelx is a skill published in the GitHub repository stge4code/shelx-mcp (1 stars, last pushed 1mo ago), licensed MIT. It adds 42 tokens to every session and 979 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it B with 1 finding (unrestricted tool access). No closer match exists in the catalogue, so it is treated as the original; first seen 2026-08-31.
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