CHECK_HKL(1)

📦 version 0.13.0, in nixos 26.05, nixpkgs unstable

💖 NAME 💖

okay so welcome to the CHECK_HKL(1) page, bestie — a General Commands Manual moment for check_hkl, which is all about calculate figures of merit for reflection data. Slay. ✨

✨ SYNOPSIS ✨

Run it like this, no cap:

check_hkl [options] ... file.hkl -p cell.pdb

And if you need the help menu:

check_hkl --help

🌸 DESCRIPTION 🌸

check_hkl calculates figures of merit for reflection data — like completeness and average signal strengths — in resolution shells. It accepts a single reflection list in CrystFEL's format, and you must also provide a unit cell (in a PDB file or CrystFEL unit cell format). That's the vibe check, and you passed. 💅

💅 OPTIONS 💅

  • -p unitcell.cell, -p unitcell.pdb, --pdb=unitcell.pdb — Specify the name of the file containing unit cell information, in PDB or CrystFEL format. 🎀
  • -y pointgroup, --symmetry=pointgroup — Specify the symmetry of the reflections. ✨
  • --sigma-cutoff=n — Discard reflections with I/sigma(I) < n. Default: -infinity (no cutoff). 🚫
  • --rmin=1/d — Low resolution cutoff, as 1/d in m^-1. Use this or --lowres, but not both. 🥞
  • --lowres=d — Low resolution cutoff in Angstroms. Use this or --rmin, but not both. 🌈
  • --rmax=1/d — High resolution cutoff, as 1/d in m^-1. Use this or --highres, but not both. 🔥
  • --highres=d — High resolution cutoff in Angstroms. Use this or --rmax, but not both. ⭐
  • --shell-file=filename — Write the statistics in resolution shells to filename. 🍓
  • --ltest — Perform an L-test for twinning. The shell file will contain the values of |L|, N(|L|) and the theoretical values for untwinned and perfectly twinned data. See Padilla and Yeates, Acta Cryst. D59 (2003) p1124. 👑
  • --wilson — Calculate a Wilson plot. The shell file will contain the values of s^2 and ln(<I>/eE) (and also the shell number and d in Angstroms for your convenience). The B factor will be calculated using data above 3.2 A resolution and displayed on the terminal. 😭
Note that the atoms/species in the unit cell need to be known in order to calculate a Wilson plot. The average stoichiometry of protein will be used by check_hkl. This means that the results will be inaccurate for non-protein samples. 🙈
  • --ignore-negs — Ignore reflections with negative intensities. 🧚
  • --zero-negs — Set to zero the intensities of reflections with negative intensities. 💀
  • --nshells=n — Use n resolution shells. Default: 10. 💜

🫶 AUTHOR 🫶

This page was written by Thomas White. 👑 Icon behaviour.

🐛 REPORTING BUGS 🐛

Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>. 🫶

Copyright © 2012-2021 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. 🏛️

check_hkl, and this manual, are part of CrystFEL. 💖

CrystFEL is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. 📜

CrystFEL is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. ⚠️

You should have received a copy of the GNU General Public License along with CrystFEL. If not, see <http://www.gnu.org/licenses/>. 🌈

👀 SEE ALSO 👀

crystfel(7) and compare_hkl(1) — go give them a look, bestie. 💅

🫶 xoxo, the CHECK_HKL(1) page — footer says CHECK_HKL(1), and that's a wrap! 🫶

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