ccd = coordinates of a chemical component from CCD or monomer library. FORMAT can be specified as one of: mmcif, mmjson, pdb, ccd (read-only). Usage: gemmi convert INPUT_FILE OUTPUT_FILE with possible conversions between PDB, mmCIF and mmJSON. It cannot recognize categories (mmJSON groups by categories),Īnd it cannot recognize numbers (so it quotes the numbers).ĬIF-JSON adds also two extra objects: “CIF-JSON” and “Metadata”. The major difference between the two is that CIF-JSON is dictionary-agnostic: When output file is -, write to standard output. Modifications: -skip-category=CAT Do not output tags starting with _CAT -sort Sort tags in alphabetical order. dot=STRING JSON representation of CIF's '.' (default: null). numb=quote|nosu|mix Convert the CIF numb type to one of: quote - string in quotes, nosu - number without s.u., mix (default) - quote only numbs with s.u. bare-tags Output tags without the first underscore. m, -mmjson Compatible with mmJSON from PDBj. JSON output options: -c, -comcifs Conform to the COMCIFS CIF-JSON standard draft. General options: -h, -help Print usage and exit. The output can be COMCIFS CIF-JSON (-c), mmJSON (-m), or a custom JSON flavor (default). Usage: gemmi cif2json INPUT_FILE OUTPUT_FILE Convert CIF file (any CIF files, including mmCIF) to JSON. For example, it cannot filter values itself, This is a minimalistic program designed to be used together with Unix Options: -h, -help display this help and exit -V, -version display version information and exit -v, -verbose print additional messages to stderr -f, -file=FILE obtain file (or PDB ID) list from FILE -name=PATTERN filename glob pattern used in recursive grep by default, *.cif and *.cif.gz files are searched -m, -max-count=NUM print max NUM values per file -O, -one-block optimize assuming one block per file -a, -and=tag Append delimiter (default ' ') and the tag value -d, -delimiter=DELIM CSV-like output with specified delimiter -n, -line-number print line number with output lines -H, -with-filename print the file name for each match -b, -no-blockname suppress the block name on output -t, -with-tag print the tag name for each match -l, -files-with-tag print only names of files with the tag -L, -files-without-tag print only names of files without the tag -c, -count print only a count of values per block or file -r, -recursive ignored (directories are always recursed) -w, -raw include '?', '.', and string quotes -s, -summarize display joint statistics for all files To change it, specify -name=* or -name=*.hkl. By default, recursive directory search checks only *.cif(.gz) files. Usage: gemmi grep TAG FILE_OR_DIR_OR_PDBID gemmi grep -f FILE TAG Search for TAG in CIF files. Apart from checking the syntax it can check most of the rules ) 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 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) validate ¶Ī CIF validator. Usage: gemmi 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. Gemmi 0.5.2 Command-line utility that accompanies the GEMMI library, which is a joint project of CCP4 and Global Phasing Ltd.
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