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Gemmi 0.7.5 documentation
Gemmi 0.7.5 documentation
  • Overview
  • Installation
    • C++ library
    • Python module
    • Fortran and C bindings
    • WebAssembly
    • Program
    • Testing
  • Gemmi program
    • validate
    • grep
    • cif2json
    • json2cif
    • cifdiff
    • convert
    • set
    • tags
    • map
    • mask
    • mtz
    • mtz2cif
    • cif2mtz
    • sf2map
    • map2sf
    • merge
    • ecalc
    • sfcalc
    • fprime
    • reindex
    • residues
    • align
    • sg
    • contents
    • contact
    • blobs
    • h
    • mondiff
    • crd
    • drg
    • wcn
    • xds2mtz

Prerequisites

  • CIF Parser
    • What are STAR, CIF, DDL, mmCIF?
    • What is parsed?
    • DOM and SAX
    • Reading and writing
    • Document
    • Block
    • Pairs and Loops
    • Column
    • Table
    • Validation
    • Design choices
    • Examples
  • Symmetry
    • Space group table
    • SpaceGroup
    • Operations
    • Groups of Operations
    • ASU
    • Twinning
    • C++ Example
    • Implementation notes
  • Math and unit cell
    • Vectors and coordinates
    • 3x3 matrices
    • Transformations
    • Box
    • Unit cell
    • Unit cell reduction
  • Miscellaneous utils
    • FASTA and PIR reader
    • Logger
    • Copy of the PDB archive
    • Directory walking
    • Input abstractions (decompressing on the fly)

Working with Molecules

  • Chemistry
    • Elements
    • Small Molecules
    • Chemical Components
    • Monomer library
    • gemmi drg: high-level overview
  • Macromolecular models
    • Coordinate files
    • Structure
    • Model
    • Chain
    • Residue
    • Atom
    • AtomAddress and CRA
    • Examples
    • Flat Structure Representation
  • Structure analysis
    • Neighbor search
    • Contact search
    • Matthews coefficient
    • Sequence alignment
    • Superposition
    • Selections (CID)
    • Selections (PyMOL syntax)
    • Graph analysis
    • Torsion angles
    • Topology
    • Modelling B-factors

Working with Data

  • Grids and maps
    • Volumetric grid
    • MRC/CCP4 maps
  • Reciprocal space
    • MTZ format
    • SF mmCIF
    • MTZ ↔ mmCIF
    • XDS_ASCII
    • SX hkl CIF
    • Resolution bins
    • Intensities
    • AsuData: merged reflections
    • Reciprocal-space grid
    • FFT
  • Scattering
    • X-ray form factors
    • Anomalous scattering
    • Electron form factors
    • Neutron scattering
    • Direct summation
    • Density for FFT
    • Mott-Bethe formula
    • Scaling and bulk solvent correction

Other Docs

  • ChangeLog
  • Python API reference
  • C++ API reference
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