gemmi(1)

✨ NAME ✨

gemmi — the CLI for the GEMMI library 💖 (and yes bestie, it's a User Commands girlie, we thrive here)

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🌸 DESCRIPTION 🌸

Okay so picture this: gemmi is a whole command-line toolkit, and it's not one thing, it's a collection. The way it works is you run gemmi and then you hand it one of these subcommands, and that subcommand does its own lil job. Crystallography, structures, maps, reflections — all of it. No cap. 🧚

🎀 Commands:

• align — sequence alignment, the global pairwise kind, with an affine gap penalty. Slay.
• blobs — lists the electron density blobs that nobody ever modelled. The unmodelled ones. Iconic.
• cif2json — translates (mm)CIF into (mm)JSON.
• cif2mtz — converts a structure factor mmCIF into MTZ.
• cifdiff — compares the tags in two (mm)CIF files, side by side, like a vibe check for tags.
• contact — searches for contacts, aka neighbouring atoms. Who's standing next to who 👀
• contents — gives you the info about the contents of a coordinate file (pdb, mmCIF, ...).
• convert — converts a file (CIF → JSON, mmCIF → PDB) or just, like, modifies the structure.
• crd — prepares a topology file (.crd) for Refmac.
• drg — fills in restraint values using AceDrg tables.
• ecalc — calculates normalized amplitudes E.
• fprime — calculates the anomalous scattering factors f' and f". Fancy.
• grep — searches for tags in CIF file(s). The CIF version of stalking, respectfully.
• h — adds or removes hydrogen atoms.
• json2cif — translates mmJSON into mmCIF.
• map — prints info about a CCP4 map, or modifies it.
• map2sf — transforms a CCP4 map into map coefficients (in MTZ or mmCIF).
• mask — makes a bulk-solvent mask in the CCP4 format.
• merge — merges or compares intensities from reflection file(s).
• mondiff — compares two monomer CIF files.
• mtz — prints info about an MTZ reflection file.
• mtz2cif — converts MTZ into structure factor mmCIF.
• reindex — reindexes an MTZ file.
• residues — lists residues from a coordinate file.
• rmsz — validates geometry using the monomer library.
• set — modifies coordinate files. Think pdbset, but make it gemmi.
• sf2map — transforms map coefficients (from MTZ or mmCIF) into a map.
• sfcalc — calculates structure factors from a model.
• sg — info about space groups.
• ss — determines the secondary structure structure of polypeptide chains.
• tags — lists tags from CIF file(s).
• validate — validates CIF 1.1 syntax.
• wcn — calculates local density / contact numbers (WCN, CN, ACN, LDM).
• xds2mtz — converts XDS_ASCII into MTZ.

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Not a single one of these got skipped, bestie. All thirty-whatever of them. Periodt. 💅

And that's the whole page! Shoutout to gemmi 0.7.5+ds, dated April 2026, living in the gemmi(1) manual. Mwah, go read your structures 🫶💖✨