PDB_TIDY(1)

💖 PDB_TIDY — the manual page, bestie edition 💖

okay so. you're here for pdb_tidy, and honestly? iconic choice. this is the manual page for pdb_tidy version 2.5.1, and I'm gonna walk you through it like we're texting at 2am. 🦋

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🌸 NAME 🌸

pdb_tidy — it's the manual page for pdb_tidy 2.5.1, and it's about to make your PDB file look immaculate. 💅

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✨ DESCRIPTION ✨

So like, heads up first, bestie — if you just ran it with --help, you got this instead:

pdb_tidy File not found or not readable: '--help'

not me getting clowned by my own tool 😭 anyway.

What pdb_tidy actually does: it modifies the file so it adheres (as much as possible, okay, it's doing its best) to the format specifications. 🎀

⚠️ Real talk though: it expects a sorted file — like, the order has to be REMARK/ATOM/HETATM/END. So if you're not sure whether your file is sorted, go run pdb_sort first, fr fr. Don't skip this. 🙈

🌈 This includes: 🌈

• Adding TER statements after chain breaks/changes 🫶
• Truncating/Padding all lines to 80 characters — yes, all of them, no line gets left behind ✨
• Adds END statement at the end of the file 👑

💀 Also: it will remove all original TER/END statements from the file. Like, gone. Poof. So if you were attached to those, this is your warning. 💀

🧚 Usage: 🧚

python pdb_tidy.py [-strict] <pdb file>

🍓 Example: 🍓

python pdb_tidy.py 1CTF.pdb python pdb_tidy.py -strict 1CTF.pdb
# does not add TER on chain breaks

^^ that -strict one, bestie? it does not add TER on chain breaks. that's the whole vibe of it. 🔥

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👑 The lore 👑

This program is part of the pdb-tools suite of utilities and should not be distributed isolatedly. periodt. ✋

The pdb-tools were created to quickly manipulate PDB files using the terminal, and — this is the slay part — they can be used sequentially, with one tool streaming data to another. it's giving pipeline main character energy. 🌈⭐

They're based on old FORTRAN77 code that was taking too much effort to maintain and compile. RIP. 😭🕯️ gone but never forgotten.

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and that's the whole page, bestie!! 💜

pdb_tidy 2.5.1 · September 2024 · PDB_TIDY(1) — mwah, go tidy something gorgeous. 💅✨🎀