PDB_SORT(1)

✨ PDB_SORT(1) ✨

okay bestie, welcome to the pdb_sort manual page — this is the User Commands corner of the man pages and honestly? it ate. sit down, grab a boba, we're reorganizing a PDB file together 🫶

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🌸 NAME 🌸

pdb_sort — the manual page for pdb_sort 2.5.1. that's it, that's the name, she's simple and she's iconic 💅

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🎀 DESCRIPTION 🎀

so like, if you ever see this:

pdb_sort Sorting key is not valid: '-'

that's her telling you the sorting key you handed over is a no. not valid, bestie. moving on 💀

pdb_sort sorts the ATOM/HETATM/ANISOU/CONECT records in a PDB file. it's giving organizational queen ✨

here's the whole sorting agenda, no cap:

• Atoms are always sorted by their serial number — meaning the original ordering of the atoms within each residue is not changed. the vibes inside a residue stay exactly as they were.
• Alternate locations are sorted by default. yes queen, default behavior, we love a default.
• Residues are sorted according to their residue sequence number, and then by their insertion code (if any). sequence number first, icode as the tiebreaker, main character energy 👑
• Chains are sorted by their chain identifier.

and then, finally, the file is sorted by all keys, and the records get placed in this exact order:

• ATOM/ANISOU, intercalated if the latter exist — HETATM — CONECT, sorted by the serial number of the central (first) atom

🚨 okay important things, listen up: MASTER, TER, and END statements are removed. literally gone. Headers (HEADER, REMARK, etc) are kept and placed first. and does NOT support multi-model files — like, at all. if you've got a multi-model file, the move is: use pdb_splitmodel, then pdb_sort on each model, and then pdb_mkensemble. do it in that order or perish 😭

🦋 Usage 🦋

python pdb_sort.py -<option> <pdb file>

🍓 Example 🍓

python pdb_sort.py 1CTF.pdb
       # sorts by chain and residues

python pdb_sort.py -C 1CTF.pdb
       # sorts by chain (A, B, C ...) only

python pdb_sort.py -R 1CTF.pdb
       # sorts by residue number/icode only

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💖 THE pdb-tools LORE 💖

this program is part of the pdb-tools suite of utilities and should not be distributed isolatedly. keep the family together fr fr 🫂

the pdb-tools were created to quickly manipulate PDB files using the terminal, and can be used sequentially, with one tool streaming data to another. pipeline queen behavior, we're obsessed 🌈

they are based on old FORTRAN77 code that was taking too much effort to maintain and compile. RIP. 🪦💐

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okay that's the whole page bestie, you're officially educated ✨ this was pdb_sort 2.5.1, September 2024, and it's PDB_SORT(1) — go sort something, slay 💅🎀🦋