NAME
gemmi - CLI for GEMMI library
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
- 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