Skip to main content
Glama

Crystallography

by io.github.pipeworx-io
OverviewDiscussionsAdmin

Get Cif

get_cif
Read-onlyIdempotent

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.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cod_idYesCOD numeric structure id, e.g. "1009000".

Schema Changelog

Changes observed during successful MCP inspections.

  1. Changed1 schema field changed
    • addedInput schema / examples
      Added value: +[
+  {
+    "cod_id": "1009000"
+  }
+]
  2. Added

TDQS

A4.3/5.0
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already indicate safe read-only behavior; description adds that it is 'Keyless' and details the return format (CIF text + parsed summary), providing additional context.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness5/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Concise and front-loaded with the core action and purpose, no unnecessary sentences.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given no output schema, the description fully explains the return contents (CIF text and summary with formula, space group, cell, atom count), making it complete.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema covers 100% of parameters with a clear description; the tool description adds minimal new info beyond 'numeric COD ID', which is already in the schema.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

Clearly states it fetches a CIF file by COD ID, specifies the content (symmetry, atoms) and distinguishes from siblings by noting it provides the real atomic structure versus metadata.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Explicitly advises using after search_structures/get_structure for atomic structure retrieval, providing clear context for when to invoke this tool.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

All Crystallography toolsInspect
Try in Browser
One endpoint for every MCP toolRayrun runs every MCP server behind one URL and holds the credentials. Each call is decided per client, tool, and argument, then recorded.ray.runAd

Glama MCP Gateway

Add one secure layer between your agents and this server.

Resources