cif

When to Use This Skill

Use this skill when:

• Parsing or generating CIF files from crystallographic databases (COD, ICSD, Materials Project)
• Validating crystal structure data for publication or submission
• Converting between CIF and other structure formats (POSCAR, XYZ, PDB)
• Extracting atomic coordinates, unit cell parameters, or symmetry information
• Implementing crystallographic software or visualization tools
• Processing Powder Diffraction File (PDF) data

Overview

The Crystallographic Information File (CIF) is the IUCr standard for representing crystallographic information. It is the universal format for exchanging crystal structure data.

Format Specification

• Encoding: ASCII text, case-insensitive tags
• Structure: Data blocks starting with data_ declarations
• Syntax: Tag-value pairs, loops for tabular data
• Comments: Lines beginning with #
• Strings: Quoted with ' or " or delimited by ; for multiline

Key Elements

Element	Description
_cell_length_a/b/c	Unit cell dimensions
_cell_angle_alpha/beta/gamma	Unit cell angles
_atom_site_label	Atom identifier
_atom_site_fract_x/y/z	Fractional coordinates
_atom_site_occupancy	Site occupancy factor
_symmetry_equiv_pos_as_xyz	Symmetry operations
_atom_site_type_symbol	Element symbol

Example Snippet

data_NaCl
_cell_length_a   5.6402
_cell_length_b   5.6402
_cell_length_c   5.6402
_cell_angle_alpha 90
_cell_angle_beta  90
_cell_angle_gamma 90
_space_group_name_H-M 'F m -3 m'

loop_
_atom_site_label
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
Na1  0.0000  0.0000  0.0000
Cl1  0.5000  0.5000  0.5000

Format Validation Tools

Tool	Purpose
checkCIF	IUCr online validation service (https://checkcif.iucr.org/)
PLATON	Structure validation and analysis
Gemmi validate	Command-line validation
PyCIFRW validation	Programmatic validation

Tools

Tool	Purpose
PyCIFRW	Python parser/writer
Gemmi	C++ library with Python bindings
Cif2Cell	Convert to computational codes
checkCIF	IUCr validation service
pycifstar	Modern Python CIF library

Usage Examples

Parse CIF with PyCIFRW

from CifFile import ReadCif

# Read a CIF file
cif = ReadCif("structure.cif")

# Access data blocks
for block_name in cif.keys():
    block = cif[block_name]
    print(f"Block: {block_name}")

    # Get cell parameters
    a = block.get('_cell_length_a')
    b = block.get('_cell_length_b')
    c = block.get('_cell_length_c')
    print(f"Cell: {a} x {b} x {c}")

    # Get atom sites
    labels = block.get('_atom_site_label')
    x = block.get('_atom_site_fract_x')
    y = block.get('_atom_site_fract_y')
    z = block.get('_atom_site_fract_z')

Parse CIF with Gemmi

import gemmi

# Read CIF file
doc = gemmi.cif.read_file("structure.cif")
block = doc.sole_block()

# Extract unit cell
cell = gemmi.UnitCell()
cell.set_from_block(block)
print(f"Cell volume: {cell.volume}")

# Convert to structure
structure = gemmi.make_structure_from_block(block)
print(f"Formula: {structure[0].formula}")

Write CIF File

from CifFile import CifFile, CifBlock

# Create new CIF
cif = CifFile()
block = CifBlock("my_structure")

# Add cell parameters
block['_cell_length_a'] = '5.0'
block['_cell_length_b'] = '5.0'
block['_cell_length_c'] = '5.0'
block['_cell_angle_alpha'] = '90'
block['_cell_angle_beta'] = '90'
block['_cell_angle_gamma'] = '90'

# Add atom data using loops
block.AddLoopItem(('_atom_site_label', ['Si1', 'O1']))
block.AddLoopItem(('_atom_site_fract_x', ['0.0', '0.5']))

cif['my_structure'] = block
cif.write_file("output.cif")

Resources

• Website: https://www.iucr.org/resources/cif