COMPARE_HKL(1)

📦 version 0.13.0, in nixos 26.05, nixpkgs unstable

💅 compare_hkl — like, the whole vibe

Hey bestie, welcome to COMPARE_HKL(1), from the General Commands Manual era of Unix docs (yes she's that girl). Buckle up, we're comparing reflection data and it's gonna slay. 🦋

✨ NAME ✨

compare_hkl — compare reflection data. That's it, that's the whole job. 💖

🎀 SYNOPSIS 🎀

compare_hkl [options] ... file1.hkl file2.hkl -p cell.pdb

compare_hkl --help

Literally just hand her two .hkl files, tell her about the unit cell, and she'll pop out figures of merit. Iconic behavior, ngl. ✨

🌸 DESCRIPTION 🌸

So. compare_hkl takes two sets of reflection data and compares them, calculating figures of merit like R-factors. 🫶

Two reflections count as equivalent based on whichever point group you pick — so choose wisely, bestie. Which means you have to give her a unit cell, either as a PDB file or as a CrystFEL unit cell file. No cell, no compari— well, you get it. 😭

💅 OPTIONS 💅

  • -y pointgroup, --symmetry=pointgroup — tells her the symmetry of the reflections. Both reflection lists have to use the same symmetry, that's the rule fr fr. Default: 1 (aka no symmetry at all, we love a low-maintenance queen).
  • -p unitcell.cell, -p unitcell.pdb, --pdb=unitcell.pdb — the name of the file with the unit cell info, either in PDB or CrystFEL format. She needs this, periodt.
  • --fom=FoM — calculate figure of merit FoM. The possible figures of merit are, and I quote:
    • Rsplit — 2^(-0.5) * sum(|I1-kI2|) / [ 0.5*sum(I1+kI2) ]
    • R1f — sum(sqrt(I1)-sqrt(kI2)) / sum(sqrt(I1))
    • R1i — sum(|I1-kI2|) / sum(I1)
    • R2 — sqrt(sum[(I1-kI2)^2] / sum(I1^2))
    • CC (CChalf) — the Pearson correlation coefficient. 📈
    • CC* (CCstar) — see Karplus and Diederichs, Science 336 (2012) p1030.
    • CCano — the correlation coefficient of the Bijvoet differences of acentric reflections.
    • CRDano — RMS anomalous correlation ratio: the anomalous differences from each data set get plotted in a scatter graph, and the variance along both diagonals is measured. See Evans, Acta Crystallographica D62 (2006) p72.
    • Rano — sum(|I+ - I-|) / 0.5*sum(I+ + I-)
Heads up bestie 🚨 — this figure of merit compares measurements within one data set, so it isn't really a "comparison" operation in the sense of "compare_hkl". She's still in compare_hkl anyway so that the ratio Rano/Rsplit can be calculated (see just below). I+ gets taken as the mean of the I+ values from both data sets, and likewise for I-.
  • Rano/Rsplit — the ratio of Rano to Rsplit, as defined above. Math girlie behavior. 🧮
  • d1sig and d2sig — the fraction of differences between intensities which are within one times (for d1sig) and two times (for d2sig) the combination of the corresponding sigma(I) values.

Okay so: I1 and I2 are the intensities of the same reflection in both reflection lists. The two sets of reflections get put on a common scale (linear and Debye-Waller terms) — unless you use -u, in which case they do not. 💀

  • --nshells=n — use n resolution shells. Default: 10.
  • -u — fix scale factors to unity. That's it. Simple queen.
  • --shell-file=filename — write the figure of merit in resolution shells to filename. Default: "shells.dat".
  • --ignore-negs — ignore reflections with negative intensities. 🙈
  • --zero-negs — set to zero the intensities of reflections with negative intensities.
  • --sigma-cutoff=n — discard reflections with I/sigma(I) < n. Default: -infinity (no cutoff, everyone's invited).
  • --rmin=1/d — low resolution cutoff, as 1/d in m<sup>-1</sup>. Use this or --lowres, but not both. Pick a lane bestie. 🎀
  • --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<sup>-1</sup>. Use this or --highres, but not both.
  • --highres=d — high resolution cutoff in Angstroms. Use this or --rmax, but not both.

👑 AUTHOR 👑

This page was written by Thomas White. Shoutout to the founder, we stan. 🫶

🌈 REPORTING BUGS 🌈

Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>. She wants to hear from you, fr fr. 💌

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

compare_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/>.

No cap: that warranty bit is not a joke, it's literally all caps in the original, so respect the drama. 🚨

⭐ SEE ALSO ⭐

crystfel(7), check_hkl(1), render_hkl(1) — go read the whole friend group, iykyk. 💅

Okay that's the whole page bestie! 🦋 This was COMPARE_HKL(1) from the General Commands Manual, © 2012-2021 DESY, Helmholtz Association — mwah, go compare some reflections, ily! 🍓✨

📦 where this page comes from