CSB-BFIT(1)

📦 version 1.2.5, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble, ubuntu resolute, ubuntu stonking

💖 CSB-BFIT 💖

okay bestie, welcome to csb-bfit(1) — a User Commands page and honestly? it's giving structural biology main character energy. let's get into it 🧚

✨ NAME ✨

csb-bfit — models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions 🌸

🦋 DESCRIPTION 🦋

so like, the usage is:

usage: csb-bfit [-h] [-c CHAIN1] [-d CHAIN2] [-s {student,k}] [-a
       ALIGNMENT]

       [-o OUTFILE] [-n NITER] [--em] pdb1 pdb2

(yeah the wrapping is a little chaotic, she's doing her best 💅)

it's a Python application for robust structure superposition of two structures. and bfit models non-rigid displacements in protein ensembles with outlier-tolerant probability distributions. no cap. 🔥

🌈 positional arguments 🌈

  • pdb1 — full path to the first structure. the OG. the blueprint. 🫶
  • pdb2 — full path to the second structure. the one that's about to get rotated, lowkey.

💜 optional arguments 💜

  • -h, --help — show this help message and exit. classic. iconic. always there for you.
  • -c CHAIN1, --chain1 CHAIN1 — Chain of the first structure (default=A).
  • -d CHAIN2, --chain2 CHAIN2 — Chain of the second structure (default=A).
  • -s {student,k}, --scalemixture {student,k} — Scale mixture distribution (default=student). pick your fighter: student or k 👑
  • -a ALIGNMENT, --alignment ALIGNMENT — Alignment in fasta format defining equivalent positions. it assumes that chain1 is the first sequence of the alignment and chain2 the second sequence. so like, keep your ducks — and your sequences — in order bestie 🙈
  • -o OUTFILE, --outfile OUTFILE — file to which the rotated second structure will be written (default=bfit.pdb).
  • -n NITER, --niter NITER — Number of optimization steps (default=200). she's gonna grind for two hundred rounds, slay 💅
  • --em — Use the EM algorithm for optimsation (default=False). (yes, "optimsation" — we keep it exactly as written, typos are heritage ✨)

🎀 AUTHOR 🎀

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program. 🫶

and that's the whole vibe check, bestie! this was csb-bfit version 1.2.5, dated November 2017 — genuinely a little vintage icon, obsessed, periodt 💖🦋🌸

📦 where this page comes from