NAME

       gemmi - CLI for GEMMI library

DESCRIPTION

   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

       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

gemmi 0.7.4+ds                                    December 2025                                         gemmi(1)