$ gemmi -h
gemmi 0.7.5
Command-line utility that accompanies the GEMMI library,
which is a joint project of CCP4 and Global Phasing Ltd.
Licence: Mozilla Public License 2.0. Copyright Global Phasing Ltd.
https://github.com/project-gemmi/gemmi

Usage: gemmi [--version] [--help] <command> [<args>]

Commands:
 align         sequence alignment (global, pairwise, affine gap penalty)
 blobs         list unmodelled electron density blobs
 cif2json      translate (mm)CIF to (mm)JSON
 cif2mtz       convert structure factor mmCIF to MTZ
 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
 drg           fill restraint values using AceDrg tables
 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 or compare intensities from reflection file(s)
 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
 set           modify coordinate files (think pdbset)
 sf2map        transform map coefficients (from MTZ or mmCIF) to map
 sfcalc        calculate structure factors from a model
 sg            info about space groups
 ss            determine secondary structure structure of polypeptide chains
 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
