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
