Enum: FileFormat

File formats used in structural biology

URI: valuesets:FileFormat

Permissible Values

Value	Meaning	Description
MRC	None	MRC format for EM density maps
TIFF	None	Tagged Image File Format
HDF5	None	Hierarchical Data Format 5
STAR	None	Self-defining Text Archival and Retrieval format
PDB	None	Protein Data Bank coordinate format
MMCIF	None	Macromolecular Crystallographic Information File
MTZ	None	MTZ reflection data format
CBF	None	Crystallographic Binary Format
DM3	None	Digital Micrograph format
SER	None	FEI series format

Slots

Name	Description
file_format	File formats used in structural biology

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: FileFormat
description: File formats used in structural biology
from_schema: https://w3id.org/linkml/valuesets
rank: 1000
permissible_values:
  MRC:
    text: MRC
    description: MRC format for EM density maps
    annotations:
      extension:
        tag: extension
        value: .mrc, .map
      applications:
        tag: applications
        value: EM volumes, tomograms
  TIFF:
    text: TIFF
    description: Tagged Image File Format
    annotations:
      extension:
        tag: extension
        value: .tif, .tiff
      applications:
        tag: applications
        value: micrographs, general imaging
  HDF5:
    text: HDF5
    description: Hierarchical Data Format 5
    annotations:
      extension:
        tag: extension
        value: .h5, .hdf5
      applications:
        tag: applications
        value: large datasets, metadata storage
  STAR:
    text: STAR
    description: Self-defining Text Archival and Retrieval format
    annotations:
      extension:
        tag: extension
        value: .star
      applications:
        tag: applications
        value: RELION metadata, particle parameters
  PDB:
    text: PDB
    description: Protein Data Bank coordinate format
    annotations:
      extension:
        tag: extension
        value: .pdb
      applications:
        tag: applications
        value: atomic coordinates, legacy format
  MMCIF:
    text: MMCIF
    description: Macromolecular Crystallographic Information File
    annotations:
      extension:
        tag: extension
        value: .cif
      applications:
        tag: applications
        value: atomic coordinates, modern PDB format
  MTZ:
    text: MTZ
    description: MTZ reflection data format
    annotations:
      extension:
        tag: extension
        value: .mtz
      applications:
        tag: applications
        value: crystallographic reflections, phases
  CBF:
    text: CBF
    description: Crystallographic Binary Format
    annotations:
      extension:
        tag: extension
        value: .cbf
      applications:
        tag: applications
        value: detector images, diffraction data
  DM3:
    text: DM3
    description: Digital Micrograph format
    annotations:
      extension:
        tag: extension
        value: .dm3, .dm4
      applications:
        tag: applications
        value: FEI/Thermo Fisher EM data
  SER:
    text: SER
    description: FEI series format
    annotations:
      extension:
        tag: extension
        value: .ser
      applications:
        tag: applications
        value: FEI movie stacks