PDB_MERGE(1)

📦
version 2.5.1 · 3 versions
, in debian trixie, ubuntu questing

💖 PDB_MERGE(1) 💖

hey bestie!! this is the manual page for pdb_merge — and yeah, we're in the User Commands corner of the man pages today. pull up a chair 🎀

✨ NAME ✨

pdb_merge — the manual page for pdb_merge 2.5.1, and also the tool itself, which is very demure, very mindful, very "smoosh your PDB files together" 💅

🌸 DESCRIPTION 🌸

okay so first thing, and I'm just gonna say it exactly how it is:

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

not me getting that as my opening line 😭 that's literally what the tool spits out. moving on! 🦋

It merges several PDB files into one. That's the whole vibe. Many files in, one file out. Queen behavior 👑

BUT. and this is the important part, bestie, listen — the contents are not sorted and no lines are deleted (like, for example, END and TER statements just stay there, chilling). So because of that, the recommendation is to pipe the results through pdb_tidy.py. fr fr, do that, your downstream self will thank you. 🫶

🌈 Usage:

python pdb_merge.py <pdb file> <pdb file>

⭐ Example:

python pdb_merge.py 1ABC.pdb 1XYZ.pdb

and now the part where I brag about the family this tool comes from:

This program is part of the pdb-tools suite of utilities and should not be distributed isolatedly. like, don't separate them, they're a unit, they're a friend group 💜

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 giving pipeline core, it's giving unix girlie excellence ✨

They are based on old FORTRAN77 code that was taking too much effort to maintain and compile. RIP. 🙏 rest in peace to the FORTRAN, you served your time.

heads up bestie: that "not sorted, no lines deleted" thing is not a cute little quirk — it's a real caveat. If you don't run this through pdb_tidy.py afterward, you're gonna have END and TER statements just hanging out wherever they landed. You've been warned 💀

and that's the whole page!! 🦋🌸💖

sign-off time: this little love letter is pdb_merge 2.5.1, and it's dated September 2024. slay, go merge something, mwah 💅🎀

📦 where this page comes from