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Validate a public PDBx/mmCIF .cif file for wwPDB DDL2 dictionary conformance, or compare two versions to see which findings regressed or resolved.
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https://powmcp.com/structure-file-check/mcp {
"mcpServers": {
"powmcp-structure-file-check": {
"type": "http",
"url": "https://powmcp.com/structure-file-check/mcp"
}
}
}Terminal agents add this app with one command:
claude mcp add --transport http powmcp-structure-file-check https://powmcp.com/structure-file-check/mcpcodex mcp add powmcp-structure-file-check --url https://powmcp.com/structure-file-check/mcpgemini mcp add --transport http powmcp-structure-file-check https://powmcp.com/structure-file-check/mcpManage, disable, or remove this connection in your agent's own MCP settings. PowMCP does not label an external connection as installed without confirmation from that client.
Proof
Validate a hosted PDBx/mmCIF structure against the wwPDB DDL2 dictionary with gemmi, with exact category-and-item evidence: real dictionary validation, not a syntax parse
Validate one public PDBx/mmCIF macromolecular structure file against the bundled wwPDB PDBx/mmCIF DDL2 dictionary using gemmi validate with exact category, item, and severity evidence, or compare two same-lineage structures across hosts or versions, with a clear dictionary-conformance-versus-structural-correctness boundary.
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structure_check
Validates one directly hosted public PDBx/mmCIF macromolecular structure file (an RCSB or PDBe .cif, fetched over HTTP(S) under a few-hundred-MB cap and magic-sniffed to start with data_) against the bundled pinned wwPDB PDBx/mmCIF DDL2 dictionary (mmcif_pdbx_v50.dic, v50), run offline in a no-network sandbox by the gemmi validate engine: real dictionary validation, not a syntax parse. Returns conformance pass/fail (conforms), the gemmi engine and dictionary versions, severity counts (error/warning), findings most-severe-first each grouped by category and item (e.g. _atom_site.group_PDB) with rule class (enumeration, data-type, regex, mandatory-item, parent-child-key, category-validity) and the gemmi message, a structural inventory (data block, entry id, experimental method, atom/chain/entity counts, audit/revision categories), distinguished states (not-a-cif vs cif-invalid; syntax-error vs dictionary-violation; item-undefined-in-dictionary vs value-out-of-enum; no-findings vs not-checked), and truncation. Use for one-structure conformance and diagnosis: 'is this .cif valid PDBx/mmCIF', 'is it wwPDB-dictionary-conformant', 'what dictionary or format problems does it have', 'is it clean enough to redeposit or archive'. A pass means only that the fetched file satisfied the pinned wwPDB DDL2 dictionary and CIF format (gemmi validate checks category/item validity, mandatory items, enumerations, data-type/regex, and parent-child key links, never whether the structure's geometry is sound, refinement is good, the model fits the density, or the structure is biologically correct), and it does not validate an unhosted local file. Downloads and validates a live structure file and can take up to 90 seconds. Tell the user before calling.
structure_compare
Runs the identical pinned gemmi validate against exactly two directly hosted public PDBx/mmCIF structure files of the SAME lineage (the same PDB entry served by two hosts (RCSB vs PDBe), two curation pipelines, or a before/after version (the version may differ)), baseline first, revised second, sequentially under one shared 115-second deadline, then reports which dictionary findings regressed or were resolved. Select this whenever two structure URLs are given for one entry and the user asks what conformance changed or which file has fewer machine-checkable findings; the tool checks lineage itself and reports the pair as not-comparable if the two files resolve to different PDB entries, so you do not need to pre-verify sameness. Returns per-file hashes, entry ids, pass verdicts and severity counts; a comparability note asserting both resolved to the same entry lineage; a difference table of finding groups introduced (regressions) and resolved keyed by category, item, and rule class; and a ranking by conformance state then fewer errors. The ranking orders machine-checkable dictionary conformance only (it never means one structure is more correct, better refined, or biologically truer), and human review remains required for both. Downloads and validates two live files and can take up to 90 seconds. Tell the user before calling.
Other apps for the jobs next to Structure File Check.
Scope and boundaries for Structure File Check.
Validate the public RCSB structure at https://files.rcsb.org/download/1CRN.cif, or compare it with PDBe's 1crn_updated.cif as a second file from the same entry lineage.
Read cifState, parseState, and checkState before conforms: only a parsed CIF receives a dictionary verdict, and conforms-with-notes may still carry advisory findings. Fix the most severe finding by rule class, item, and line, then rerun; truncated findings are incomplete. Conformance covers the pinned wwPDB dictionary only, not geometry, refinement quality, density fit, or biological correctness.
Only directly hosted public, uncompressed PDBx/mmCIF files beginning with data_ are accepted. Passing the pinned wwPDB DDL2 dictionary checks does not establish sound geometry, refinement quality, fit to experimental density, or biological correctness, and maxFindings can truncate evidence.