gemmi(1)

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

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