PDB_GAP(1)

✨ PDB_GAP 💖

okay bestie, so this is the manual for pdb_gap, version 2.5.1, and it's giving "little tool, big power" energy. 🫶

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🌸 NAME 🌸

pdb_gap — manual page for pdb_gap 2.5.1

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🎀 DESCRIPTION 🎀

So the very first thing the page says is this, and I'm just gonna hand it to you exactly as-is because it's iconic in a cursed way:

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

Yeah. That's literally the first line. Moving on, bestie. 😭

pdb_gap</purl> finds gaps between consecutive protein residues in the PDB. That's the whole job. That's the assignment. 💅

It detects those gaps two ways:

• by a distance criterion, or
• by discontinuous residue numbering.

Heads up though — this only applies to protein residues. Nucleic acids, ligands, waters, whatever else you dragged in? Not the vibe here. Only proteins, periodt. 🧬

🦋 Usage:

python pdb_gap.py <pdb file>

🌈 Example:

python pdb_gap.py 1CTF.pdb

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👑 THE SUITE LORE 👑

This program is part of the pdb-tools suite of utilities and should not be distributed isolatedly. Fr fr, don't split the group up, they're a unit. 🫶

The pdb-tools were created to quickly manipulate PDB files using the terminal, and they can be used sequentially, with one tool streaming data to another. It's a whole pipeline moment, main character energy. ✨

They are based on old FORTRAN77 code that was taking too much effort to maintain and compile. 😩 Rest in peace to that legacy code honestly. RIP. 🪦💐

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vibe check recap: proteins only, two gap-detection methods, stream it, pipe it, don't ship it alone. iykyk 💖

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okay that's the whole page bestie, love u, go find those gaps 🦋

pdb_gap 2.5.1 — September 2024 — PDB_GAP(1) 🎀 mwah, slay, bye 💅