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

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