Man page - gemmi(1)

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Package: gemmi
apt-get install gemmi

Manuals in package:

Documentations in package:

gemmi - CLI for GEMMI library

	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

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 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

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)

xds2mtz

convert XDS_ASCII to MTZ