CHECK_HKL(1)

NAME
check_hkl - calculate figures of merit for reflection data

SYNOPSIS

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

check_hkl --help

DESCRIPTION
check_hkl calculates figures of merit for reflection data, such as completeness and average signal strengths, in resolution shells. check_hkl 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).

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.

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

COPYRIGHT AND DISCLAIMER
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)