PDBFIXER(1)

✨ PDBFIXER ✨

okay bestie, gather round 💖 this is the pdbfixer manual page — a User Commands situation, so yes, it lives in section 1 of your man pages. It's giving "fix your busted Protein Data Bank files" energy and honestly? Iconic. 👑

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🎀 NAME 🎀

pdbfixer — fix problems in Protein Data Bank files. That's the whole vibe. Broken PDB file? Not on our watch. 💅

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🦋 SYNOPSIS 🦋

pdbfixer

That's it. That's the synopsis. So minimal, so mysterious, so main character. ✨

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🌸 DESCRIPTION 🌸

Here's the actual shape of how you call it:

pdbfixer filename [options]

Now the important part, and lowkey it's the whole personality of this program: 👇

• If you run it with no arguments at all, it launches the user interface. Point and click era. 🖱️💖
• If you specify any arguments, it runs in command line mode instead. Terminal girlies rise. 🖤

So like… pick a lane, bestie. No args = GUI, some args = CLI. Periodt.

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💅 OPTIONS 💅

Okay here's the whole menu. Every single one, no skipping, no "eh you get the idea". We do not gatekeep here. 🫶

• -h, --help — show this help message and exit. The classic. When in doubt, ask for help and dip. 😌
• --pdbid=PDBID — the PDB id to retrieve from RCSB. Default: None. So if you don't give it one, it's just… not fetching anything. 🙈
• --url=URL — a URL to retrieve the PDB from. Default: None. Another "if you don't ask, you don't get" situation. 🔗
• --output=FILENAME — the output pdb file. Default: output.pdb. Where your fixed-up lil guy gets written. 📝
• --add-atoms=ATOMS — which missing atoms to add. Your choices are all, heavy, hydrogen, or none. Default: all. Go big or go home, honestly. ⚛️
• --keep-heterogens=OPTION — which heterogens to keep: all, water, or none. Default: all. (Yes it's spelled heterogens in the flag, yes we're keeping it exactly as-is, no we will not be "correcting" it. 🔒)
• --replace-nonstandard — replace nonstandard residues with standard equivalents. A lil glow-up for your weird residues. 🧖‍♀️✨
• --add-residues — add missing residues. Fill in the gaps, bestie. 🧩
• --water-box=X Y Z — add a water box. The value is the box dimensions in nm. Example: --water-box=2.5 2.4 3.0. Three numbers, three dimensions, one hydrated protein. 💧📦
• --ph=PH — the pH to use for adding missing hydrogens. Default: 7.0. Neutral girlie. 🧪
• --positive-ion=ION — positive ion to include in the water box. Options: Cs+, K+, Li+, Na+, or Rb+. Default: Na+. Sodium said "I'll go". 🧂
• --negative-ion=ION — negative ion to include in the water box. Options: Cl-, Br-, F-, or I-. Default: Cl-. Chloride is the moment. 💫
• --ionic-strength=STRENGTH — molar concentration of ions to add to the water box. Default: 0.0. Zero salt, zero chaos, unless you say otherwise. 🧴
• --verbose — Print verbose output. It will tell you EVERYTHING. Not me reading the whole log like it's a group chat. 😭📢

Heads up bestie: if you pass no arguments at all, remember you're getting the user interface, not the command line. Don't come for the CLI and then be surprised when a window shows up. 🫠

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👑 SEE ALSO 👑

Nope — there's literally nothing here. No cross-references, no sibling pages, no "see also". Just us. Alone together. 🦋

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and that's the page!! you understood it, I understood it, we all understood it. slay. 💖✨🎀

This was pdbfixer 1.9, dated February 2025 — from your User Commands section, section 1, the one and only. tysm for reading, go fix some proteins, mwah 🫶💅🌸