LMucko/crystallography-open-database

Crystallography Open Database (COD) — Full Snapshot

A complete mirror of the Crystallography Open Database (COD) as a single Parquet file, combining all crystallographic metadata with the raw CIF file content in one queryable dataset.

Snapshot Details

Field	Value
Snapshot date	2026-07-06
Metadata fetched	2026-07-06 18:51 (UTC+2) — 533,486 entries
CIF files downloaded	2026-07-06 18:34–21:58 — 533,862 files
Total rows	533,486 (metadata) — 411 on-hold entries excluded
File format	Parquet (zstd compressed)
License	CC0 1.0 (Public Domain)

Dataset Structure

One Parquet file (cod_full.parquet) with 75 columns — the 74 COD metadata fields plus a cif_text column containing the full raw CIF file content as a string.

Metadata Columns

Column	Type	Description
file	int64	COD ID (7-digit identifier, e.g. 1553769)
a, b, c	double	Unit cell lengths (Å)
siga, sigb, sigc	double	Standard uncertainties on cell lengths
alpha, beta, gamma	double	Unit cell angles (°)
sigalpha, sigbeta, siggamma	double	Standard uncertainties on cell angles
vol	double	Unit cell volume (ų)
sigvol	double	Standard uncertainty on volume
celltemp	double	Cell measurement temperature (K)
sigcelltemp	double	SU on cell temperature
diffrtemp	double	Diffraction measurement temperature (K)
sigdiffrtemp	double	SU on diffraction temperature
cellpressure	double	Cell measurement pressure (kPa)
sigcellpressure	double	SU on cell pressure
diffrpressure	double	Diffraction measurement pressure (kPa)
sigdiffrpressure	double	SU on diffraction pressure
thermalhist	string	Thermal history
pressurehist	string	Pressure history
compoundsource	string	Source of compound
nel	string	Number of distinct elements
sg	string	Space group (Hermann-Mauguin)
sgHall	string	Space group (Hall notation)
sgNumber	int64	Space group number (1–230)
commonname	string	Common name
chemname	string	Chemical name
mineral	string	Mineral name
formula	string	Chemical formula (sum)
calcformula	string	Calculated formula
cellformula	string	Unit cell formula
Z	int64	Number of formula units per unit cell
Zprime	double	Z′ (Z per asymmetric unit)
acce_code	string	CCDC accession code
authors	string	Publication authors
title	string	Publication title
journal	string	Journal name
year	int64	Publication year
volume	int64	Journal volume
issue	string	Journal issue
firstpage	string	First page
lastpage	string	Last page
doi	string	Digital Object Identifier
method	string	Structure determination method
radiation	string	Radiation type
wavelength	double	Wavelength (Å)
radType	string	Radiation type (detailed)
radSymbol	string	Radiation symbol
Rall	double	R-factor (all reflections)
Robs	double	R-factor (observed reflections)
Rref	double	R-factor (refined)
wRall	double	Weighted R-factor (all)
wRobs	double	Weighted R-factor (observed)
wRref	double	Weighted R-factor (refined)
RFsqd	double	R-factor on F²
RI	double	R-factor (intensity)
gofall	double	Goodness of fit (all)
gofobs	double	Goodness of fit (observed)
gofgt	double	Goodness of fit (I > 2σ(I))
gofref	double	Goodness of fit (refined)
duplicateof	int64	COD ID of which this is a duplicate
optimal	int64	Flag for optimal structure
status	string	Status (e.g. warnings)
flags	string	Status flags
text	string	Concatenated bibliography text
svnrevision	int64	SVN revision of the COD entry
date	string	Deposition date (YYYY-MM-DD)
time	string	Deposition time (HH:MM:SS)
onhold	string	On-hold release date (empty if released)

CIF Text Column

Column	Type	Description
cif_text	string	Full raw CIF file content (text)

Each CIF contains:

• Unit cell parameters and standard uncertainties
• Space group information (Hermann-Mauguin, Hall, IT number)
• Atomic site coordinates (fractional) with displacement parameters
• SHELX .res file (refinement details, atom lists, restraints)
• SHELX .hkl file (observed structure factors — Fobs)
• Publication metadata and COD database codes

Loading

from datasets import load_dataset

ds = load_dataset("your-username/cod", split="train")
print(ds[0]["formula"])      # e.g. "C16 H11 F N2 O"
print(ds[0]["sg"])           # e.g. "P 1 21/c 1"
print(ds[0]["cif_text"][:200])  # first 200 chars of the CIF

Or directly with PyArrow / DuckDB for out-of-core querying:

import pyarrow.parquet as pq

table = pq.read_table("cod_full.parquet", columns=["file", "formula", "sg", "year"])

SELECT file, formula, sg, year
FROM 'cod_full.parquet'
WHERE year >= 2020 AND sgNumber = 14
LIMIT 10;

Parsing CIF Text

For crystallographic analysis, parse cif_text with:

# gemmi (fastest, C++ bindings)
import gemmi
doc = gemmi.cif.read_string(row["cif_text"])
block = doc[0]

# pymatgen (full crystallography)
from pymatgen.core import Structure
import io
struct = Structure.from_str(row["cif_text"], fmt="cif")

Coverage

• Earliest publication: 1915
• Peak deposition years: 2012–2015 (~25–28K structures/year)
• Recent deposits: ~10K/year
• Compound types: organic, inorganic, metal-organic, minerals (excluding biopolymers)
• Data sources: CCDC, AMCSD, IUCr journals, direct depositions

License

All data in the COD is dedicated to the public domain under CC0 1.0.

Users of the data should acknowledge the original authors of the structural data. The authors, title, journal, year, and doi columns are provided for this purpose.

Citation

If you use this dataset, please cite the COD:

Grazulis, S., Chateigner, D., Downs, R. T., Yokochi, A. F. T., Quirós, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le Bail, A. (2009). Crystallography Open Database – an open-access collection of crystal structures. J. Appl. Cryst. 42, 726–729. doi:10.1107/S0021889809016690

Merkys, A., Vaitkus, A., Butkus, J., Okulič-Kazarinas, V., Kairys, V. & Gražulis, S. (2016). COD::CIF::Parser: an error-correcting CIF parser for the Perl language. J. Appl. Cryst. 49, 292–301. doi:10.1107/S1600576716000414

Source

• Website: https://www.crystallography.net/
• SQL database: sql.crystallography.net (user: cod_reader, database: cod)
• Rsync: rsync://www.crystallography.net/cif/