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compare_hkl: compare reflection data

Synopsis

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

Description

compare_hkl compares two sets of reflection data and calculates figures of merit such as R-factors. Reflections will be considered equivalent according to your choice of point group. You need to provide a unit cell, as a PDB file or a CrystFEL unit cell file.

Options

-y --symmetry=pointgroup

Specify the symmetry of the reflections. The symmetry must be the same for both lists of reflections. Default: 1 (no symmetry).

-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.

--fom=FoM

Calculate figure of merit FoM. Possible figures of merit are:

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(I₁²))
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 are plotted in a scatter graph, and the variance along both diagonals measured. See Evans, Acta Crystallographica D62 (2006) p72.
Rano: sum(|I₊ - I_-|) / 0.5*sum(I₊ + I_-).

Note that this figure of merit compares measurements within one data set, so it isn't really a "comparison" operation in the sense of "compare_hkl". It is nevertheless included in compare_hkl so that the ratio Rano/Rsplit can be calculated (see below). I₊ will be taken to be 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.
d1sig and d2sig: The fraction of differences which are within one times (for d1sig) and two times (for d2sig) the combination of the corresponding sigma(I) values.

I₁ and I₂ are the intensities of the same reflection in both reflection lists. The two sets of reflections will be put on a common scale (linear and Debye-Waller terms) unless you use -u.

--nshells=n

Use n resolution shells. Default: 10.

-u

Fix scale factors to unity.

--shell-file=filename

Write the statistics in resolution shells to filename.

--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).

--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.

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/.