PDB_SELELEM(1)

💖 PDB_SELELEM 💖

okay so bestie, welcome to pdb_selelem — it's the little element-picker from the pdb-tools fam, version 2.5.1, manual page PDB_SELELEM(1), living in the User Commands section. it is literally your girl for grabbing atoms by element. sit down, hydrate, let's go 🫶

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✨ NAME ✨

pdb_selelem — the manual page for pdb_selelem 2.5.1, and no, we're not being modest about it 💅

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🌸 DESCRIPTION 🌸

So like. When you run it with something it doesn't vibe with, it will yell at you like this:

pdb_selelem Element name is invalid: '-HELP'

and honestly? fair.

What it actually does: it selects all the atoms that match the element(s) you give it in the PDB file. that's the whole thing, that's the assignment, and it ate 🔥

And listen — the elements are read from the element column. Not vibes. Not guesses. The element column. periodt.

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🎀 Usage: 🎀

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

like, that's it. that's the whole syntax bestie, it's giving minimalist 👑

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🦋 Example: 🦋

Select all the protons, easy:

python pdb_selelem.py -H 1CTF.pdb
       # selects all protons

Select all the nitrogens, also easy:

python pdb_selelem.py -N 1CTF.pdb
       # selects all nitrogens

And the combo move — protons AND nitrogens, we love a multitasker:

python pdb_selelem.py -H,N 1CTF.pdb
       # selects all protons and nitrogens

🌈 notice how you just chain them with a comma in -H,N. iconic behaviour. no cap.

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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. like, she has a family, she has a group chat, she does not travel alone 🙈

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 situation, very main character energy, one tool hands off to the next like a relay race ✨

And they're based on old FORTRAN77 code that was taking too much effort to maintain and compile.

RIP. 💀🕯️

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that's the whole page bestie, go select some elements, you're gonna slay 💖✨🎀🦋🌸💅🫶

pdb_selelem 2.5.1 — September 2024 — PDB_SELELEM(1) and that's the sign-off, mwah 💋