---
name: "gemmi"
section: "1"
platform: "linux"
package: "gemmi"
version: "0.6.5+ds-3"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gemmi"
---

# gemmi(1)

CLI for GEMMI library

## NAME

gemmi - CLI for GEMMI library

## DESCRIPTION

### Commands:

- align

  sequence alignment (global, pairwise, affine gap penalty)

- blobs

  list unmodelled electron density blobs

- cif2mtz

  convert structure factor mmCIF to MTZ

- cif2json

  translate (mm)CIF to (mm)JSON

- cifdiff

  compare tags in two (mm)CIF files

- contact

  searches for contacts (neighbouring atoms)

- contents

  info about content of a coordinate file (pdb, mmCIF, ...)

- convert

  convert file (CIF - JSON, mmCIF - PDB) or modify structure

- crd

  prepare topology file (.crd) for Refmac

- ecalc

  calculate normalized amplitudes E

- fprime

  calculate anomalous scattering factors f' and f"

- grep

  search for tags in CIF file(s)

- h

  add or remove hydrogen atoms

- json2cif

  translate mmJSON to mmCIF

- map

  print info or modify a CCP4 map

- map2sf

  transform CCP4 map to map coefficients (in MTZ or mmCIF)

- mask

  make a bulk-solvent mask in the CCP4 format

- merge

  merge intensities from multi-record reflection file

- mondiff

  compare two monomer CIF files

- mtz

  print info about MTZ reflection file

- mtz2cif

  convert MTZ to structure factor mmCIF

- reindex

  reindex MTZ file

- residues

  list residues from a coordinate file

- rmsz

  validate geometry using monomer library

- sf2map

  transform map coefficients (from MTZ or mmCIF) to map

- sfcalc

  calculate structure factors from a model

- sg

  info about space groups

- tags

  list tags from CIF file(s)

- validate

  validate CIF 1.1 syntax

- wcn

  calculate local density / contact numbers (WCN, CN, ACN, LDM)

- xds2mtz

  convert XDS\_ASCII to MTZ