pdb2cif(1)

💖 pdb2cif — the PDB-to-mmCIF glow-up tool 💖

okay bestie, listen. this is a User Command situation, it's pdb2cif, and it lives in the cif-tools universe. she's giving converter energy, and honestly? she ate. 🎀

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✨ NAME ✨

pdb2cif — convert the content of a PDB file into mmCIF format 🦋

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✨ SYNOPSIS ✨

pdb2cif [OPTION] input [output]

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✨ DESCRIPTION ✨

so this tool attempts to write out the contents of a PDB file in mmCIF format. that's the whole mission. that's the vibe. 💅

but ngl, turning a PDB file into mmCIF format is not trivial. not even a little. the numbering schemes differ between the two, and in some cases it's literally necessary to do a sequence alignment just to recover the correct sequence numbers. it's giving detective work. it's giving archaeology. 😭

here's the tea though: when CCP4 is installed and sourced correctly, this tool will use the information in the CCP4 monomers library to guide the construction of a correct mmCIF file. iconic behavior. but in the absence of CCP4? a best effort is done. we do what we can, fr fr. 🫶

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✨ OPTIONS ✨

if no output file is given, the result gets printed to stdout. and yes — both the input and output files can be compressed. obsessed. 🌸

• --dict=<file> — specify a dictionary file containing restraints for residues specific to this file 👑
• --validate — validate the file before writing the output 🙈
• --verbose,-V — be more verbose, which is useful to diagnose validation errors 🔍

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✨ AUTHOR ✨

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

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✨ REPORTING BUGS ✨

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

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✨ SEE ALSO ✨

cif-diff, cif-grep, cif-merge, cif-validate, cif2pdb, mmcql. ✨

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lowkey the whole gang is here, go check them out, iykyk 🌈

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okay that's the whole page bestie, go forth and convert responsibly 💖✨ and for the record, this was version 2.0.0, dated 2022-11-20 — slay, periodt. 👑