PDB_DELELEM(1)

✨ NAME ✨

okay so bestie, this is pdb_delelem 💅 — that's the manual page for pdb_delelem version 2.5.1, living in section 1 of the manual (User Commands, iykyk). She deletes atoms. That's the whole vibe.

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🌸 DESCRIPTION 🌸

not the error message coming for us first but okay:

pdb_delelem Element name is invalid: '-HELP'

Anyway. What she actually does: deletes all atoms matching the given element in the PDB file. periodt. 💖

And where does she find those elements, you ask? Elements are read from the element column. no cap, that's the source of truth right there. 🦋

🎀 Usage:

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

🍓 Example:

python pdb_delelem.py -H 1CTF.pdb
       # deletes all protons

python pdb_delelem.py -N 1CTF.pdb
       # deletes all nitrogens

python pdb_delelem.py -H,N 1CTF.pdb
       # deletes all protons and nitrogens

look at her stacking elements with a comma, she's so versatile, main character energy fr fr 😭💅

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🌈 The lore (iykyk)

This program is part of the pdb-tools suite of utilities and should not be distributed isolatedly 🙈 — she's a package deal, she doesn't do solo careers.

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. pipes? we love pipes. the way that one tool just hands off to the next… obsessed. 🔥

They are based on old FORTRAN77 code that was taking too much effort to maintain and compile. RIP. 🪦✨ gone but not forgotten, she ate and left no crumbs.

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quick vibe check: she reads the element column, so if your element column is a mess, that's between you and your PDB file, bestie 🫶

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and that's the whole page! 🎀

signing off: this was pdb_delelem 2.5.1, from September 2024 💖 stay hydrated, delete your protons responsibly, and remember — pdb-tools forever, FORTRAN77 never 🌸👑