FINDWATERS(1)

📦 version 1.1.18, in debian trixie, ubuntu questing, ubuntu resolute, ubuntu stonking

💧 FINDWATERS(1) — general commands manual, section 1, bestie 💧

okay so. sit down. hydrate. we're doing findwaters today and honestly? it's giving little-guy-big-job. 🫶

✨ NAME ✨

findwaters — locate water sites in an electron density map 🌊

like. it finds the waters. that's the whole thing. she's simple, she's iconic, she's hydrated. 💅

🦋 SYNOPSIS 🦋

findwaters [options]

that's it. that's the girl. options go brrr. 🎀

🌸 DESCRIPTION 🌸

bestie, here's the tea, and I'm gonna read it to you exactly as it's written: this page says findligand is a part of the Coot suite of programs. yes, findligand. on the findwaters page. not me noticing. 🙈 I am NOT editing the source material, that's not my job, I just report the facts and the facts are what they are. 😭

anyway the point stands: this whole thing lives in the Coot</> suite of programs, iykyk. 👑

💖 OPTIONS 💖

okay so these programs follow the usual GNU command line syntax, and long options start with two dashes (-). literally the standard situation. a summary of options is included below, and yes we are going through every single one, no skipping, no summarising, we don't do that here. 🌈

  • --pdbin=file — the name of the file containing your protein structure. your main character, basically. 🧚
  • --hklin=file — the name of the input MTZ file. you gotta specify the column labels for F and PHI using the --f and --phi options. alternatively, you can input an electron density map using the --mapin option instead. pick your lane, bestie. ✨
  • --f=label — the label of the MTZ file column containing your structure factor amplitudes. the F. the drama. 💜
  • --phi=label — the label of the MTZ file column containing your structure factor phase. the PHI. the other half of the situationship. 💫
  • --pdbout=file — the output file for the waters. where the found lil guys go to live. 🍓
  • --sigma=level — the sigma level. default is 2.0. that's the vibe check threshold fr fr. 🔥
  • --flood — fills everything with water molecules. not just the water peaks. EVERYTHING. girl is not being subtle about it. 🌊🌊🌊
  • --flood-atom-radius=radius — adjusts the contact distance. default is 1.4A. personal space setting, lowkey. 🫶
  • --chop — removes water molecules below a given sigma-level. and heads up: in this case, the modified input coordinates will be written to the file specified by --pdbout. so like. it's not just deleting, it's writing too. iconic behaviour. ✂️
  • --mapin=file — the name of a CCP4 format map file. this one can be used instead of --hklin, --f and --phi. one option to rule them all, no cap. 👑
ok wait, quick vibe check: --hklin/--f/--phi are one way in, --mapin is the other way in. don't do both and then act surprised. that's the whole bit. 💀

👀 SEE ALSO 👀

the friend group!! go say hi!! 💖

🌟 AUTHOR 🌟

findwaters is written by Paul Emsley</> 👑

this manual page was written by Morten Kjeldgaard</> <mok@bioxray.dk> 💌

and that's the whole page, bestie!! it's dated January, 2011, and it came to you straight from the FINDWATERS(1) corner of the General Commands Manual. drink some water (the irony is not lost on me 🌊), stan Paul Emsley, and go find those peaks. periodt. 💅✨🎀

📦 where this page comes from