cif-merge(1)

📦
version 2.0.0 · 3 versions
, in ubuntu stonking

💖 cif-merge(1) — the girlies are merging mmCIF files 💖

okay so this is a User Commands page for cif-merge, section 1 of the manual, and bestie, you're gonna want to sit down for this one because it's lowkey a lifesaver.

✨ NAME ✨

cif-merge — merge the content of a modified PDB file into a mmCIF file 🧚

🌸 SYNOPSIS 🌸

cif-merge [options] input-file donor-file [output-file]

🦋 DESCRIPTION 🦋

so here's the tea, and it's kind of annoying ngl: a LOT of tools in the crystallographic area are still not capable of working with mmCIF files in a proper way, which means you're forced to feed them PDB files. 😭 and when they do support mmCIF? they write out mutilated files without lots of the original information contained in the input file. it's giving disrespectful, honestly.

to remedy this, cif-merge can be used to create a new mmCIF file containing information from the processed PDB (or mmCIF) file and fill in the blanks using a donor mmCIF file. 🫶 like, bestie's here to patch up your file. iconic behaviour only.

the input-file is the file that was processed by an old tool, missing the additional data. the donor-file contains the extra information to be copied. and when output-file is not specified, the result is written to stdout — so it just vibes right out at you. ✨

💅 OPTIONS 💅

  • --verbose, -v — be more verbose, which is useful to diagnose validation errors. basically it tells you why the vibe check failed. 💀

👑 AUTHOR 👑

Written by Maarten L. Hekkelman <maarten@hekkelman.com>

🎀 REPORTING BUGS 🎀

Report bugs at https://github.com/PDB-REDO/cif-tools/issues

not me asking you to file a proper bug report but... yes. do it. the devs deserve it, and so does your bug. 🐛💖

🌈 SEE ALSO 🌈

cif-diff, cif-grep, cif-validate, cif2pdb, mmcql, pdb2cif.

okay that's the whole page, no skips, no cuts, all facts intact, periodt. 💜

version 2.0.0 — dated 2022-11-20 — and this was cif-merge(1). byeeee, go merge something pretty 🌸✨

📦 where this page comes from