.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH gemmi "1" "May 2024" "gemmi 0.6.5+ds" "User Commands"
.SH NAME
gemmi \- CLI for GEMMI library
.SH DESCRIPTION
.SS "Commands:"
.TP
align
sequence alignment (global, pairwise, affine gap penalty)
.TP
blobs
list unmodelled electron density blobs
.TP
cif2mtz
convert structure factor mmCIF to MTZ
.TP
cif2json
translate (mm)CIF to (mm)JSON
.TP
cifdiff
compare tags in two (mm)CIF files
.TP
contact
searches for contacts (neighbouring atoms)
.TP
contents
info about content of a coordinate file (pdb, mmCIF, ...)
.TP
convert
convert file (CIF \- JSON, mmCIF \- PDB) or modify structure
.TP
crd
prepare topology file (.crd) for Refmac
.TP
ecalc
calculate normalized amplitudes E
.TP
fprime
calculate anomalous scattering factors f' and f"
.TP
grep
search for tags in CIF file(s)
.TP
h
add or remove hydrogen atoms
.TP
json2cif
translate mmJSON to mmCIF
.TP
map
print info or modify a CCP4 map
.TP
map2sf
transform CCP4 map to map coefficients (in MTZ or mmCIF)
.TP
mask
make a bulk\-solvent mask in the CCP4 format
.TP
merge
merge intensities from multi\-record reflection file
.TP
mondiff
compare two monomer CIF files
.TP
mtz
print info about MTZ reflection file
.TP
mtz2cif
convert MTZ to structure factor mmCIF
.TP
reindex
reindex MTZ file
.TP
residues
list residues from a coordinate file
.TP
rmsz
validate geometry using monomer library
.TP
sf2map
transform map coefficients (from MTZ or mmCIF) to map
.TP
sfcalc
calculate structure factors from a model
.TP
sg
info about space groups
.TP
tags
list tags from CIF file(s)
.TP
validate
validate CIF 1.1 syntax
.TP
wcn
calculate local density / contact numbers (WCN, CN, ACN, LDM)
.TP
xds2mtz
convert XDS_ASCII to MTZ