The full upstream README, mirrored here for reference. Install config, tool schemas, adoption signals, and an original overview live on the Crystallography listing page.
Crystallography Open Database (COD) MCP.
Part of Pipeworx — an MCP gateway connecting AI agents to 1476+ live data sources.
| Tool | Description |
|---|---|
search_structures | Search the Crystallography Open Database (COD), an open repository of crystal structures (inorganic, organic, metal-organic, and mineral). Search by compound name (free text), chemical formula, or mineral name; returns matching crystal structures with unit-cell parameters, space group, year, and a link to the CIF structure file. Keyless. Provide at least one of query, formula, or mineral. Formulas are normalized to COD's stored Hill notation for you, so "NaCl", "SiO2" and "CaCO3" all work; the response reports formula_searched with the exact string that was matched. |
get_structure | Look up a single crystal structure in the Crystallography Open Database (COD) by its numeric COD ID (e.g. "1009000"). Returns the compound/mineral name, chemical formula, space group, full unit-cell parameters (a, b, c, alpha, beta, gamma, volume), bibliographic details (title, authors, journal, year, DOI), and a link to the CIF structure file. Keyless. |
get_cif | Fetch the full CIF (Crystallographic Information File) for a COD structure by its numeric COD ID — the actual machine-readable structure: symmetry operations and the atom sites (element, fractional x/y/z coordinates, occupancy). Use after search_structures/get_structure when you need the real atomic structure, not just the metadata/link. Returns the CIF text plus a parsed summary (formula, space group, cell, atom count). Keyless. |
Add to your MCP client (Claude Desktop, Cursor, Windsurf, etc.):
tools/list at https://gateway.pipeworx.io/crystallography/mcp returns the tools in the table
above plus the shared Pipeworx meta-tools — ask_pipeworx,
discover_tools, search_within, remember/recall and the rest of the
gateway-wide set. So the tool count you see is larger than this table: a
single-pack endpoint currently lists roughly 30 shared tools alongside the
pack's own. The connection's initialize response states its exact scope, and
is the authoritative answer for a given day.
This is deliberate, not multiplexing by accident. The meta-tools are what let a
scoped connection answer a question this pack does not cover — via
ask_pipeworx, which routes across the whole catalog — without you adding a
second MCP server. There is currently no way to mount a pack endpoint without
them; if the extra schemas cost you more context than the routing is worth,
connect to the full gateway once rather than to several pack endpoints.
Or connect to the full Pipeworx gateway to get every pack's tools listed directly, instead of just this one's:
Both URLs reach the same gateway and the same 1476+ data sources. The
only difference is which pack's tools are listed directly; ask_pipeworx
reaches all of them from either one.
Instead of calling tools directly, you can ask questions in plain English — this works on the pack endpoint above as well as on the full gateway:
The gateway picks the right tool and fills the arguments automatically.
MIT