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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 the unit cell information, in PDB or CrystFEL format.

-y -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 s² 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

Copyright and Disclaimer

Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors.

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/.