gemmi

NAME

gemmi - CLI for GEMMI library

SYNOPSIS

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

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

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

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

prep

prepare topology file (.crd) for Refmac

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)