COILS-WRAP(1)

📦
version 2002 · 3 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

✨ COILS-WRAP 💅 — the manual page bestie

okay so you found coils-wrap in the User Commands section of the manual, and honestly? she's a little diva with a big job. let's get into it 🧚

🌸 NAME 🌸

coils-wrap — runs ncoils three times to give you a three-window output ✨

🎀 SYNOPSIS 🎀

coils-wrap [OPTION]

💖 DESCRIPTION 💖

so like, here's the whole vibe: coils-wrap runs ncoils three times to give you a three-window output. that's literally the entire personality. three windows. icon behavior. 👑

and if you're sitting there like "bestie what even IS ncoils" — okay so ncoils is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. then, by comparing this score to the distribution of scores in globular and coiled-coil proteins, the program calculates the probability that the sequence will adopt a coiled-coil conformation. like, it's doing protein astrology but with math and it's accurate. 🔮

✨ OPTIONS ✨

  • -i — input file in FASTA format 🍓 (yes, FASTA. not pasta. i know. devastating.)
  • -o — output file 💾
  • -r — raw output file, default: <output file>_raw 📝
  • -m — matrix type; set matrix (MTK or MTIDK) 🧬
  • -w — weight a&d = b,c,e,f&g (boolean) ⚖️
lowkey important: -w is a boolean, so it's giving on/off, not a value. don't try to hand it a number, she will simply not know what to do with it 🙈

🌈 EXAMPLES 🌈

here's the whole thing in action, copy-paste ready, no cap:

coils-wrap -m MTIDK -i /usr/share/doc/ncoils/1srya.fa -o /tmp/coils.out
-r /tmp/coils_raw.txt && less /tmp/coils.out /tmp/coils_raw.txt

and the raw ncoils call if you wanna go straight to the source:

ncoils -win 14 < /usr/share/doc/ncoils/1srya.fa

see how the first one chains into less? that's the "run it then immediately read it" pipeline, and honestly? obsessed. 🔥

🦋 FILES 🦋

  • /usr/share/coiledcoils/*.mat — matrix data files 💜

👑 AUTHOR 👑

R.B. Russell, A.N. Lupas, 1999

living legends, fr fr.

GPL

Based on Lupas, Van Dyck & Stock (1991) Science 252,1162-1164

the GPL is a real license with real rules — go read it before you go wild with redistribution, bestie. no cap. 📜

⭐ SEE ALSO ⭐

and the science, because we stan citations:

  • A Lupas: Prediction and Analysis of Coiled-Coil Structures. Methods in Enzymology, 266, 513-525, 1996
  • A. Lupas, M. Van Dyke, and J. Stock: Predicting coiled coils from protein sequences. Science, 252, 1162-1164, 1991

okay that's the whole page, you're officially educated 🎓✨ this lil manual came from 2002 and got its glow-up dated 2021-08-15, and it's filed under COILS-WRAP(1) — go forth and wrap those coils, you main character 🫶💖

📦 where this page comes from