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

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.

`-y`

--symmetry=pointgroupSpecify 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.pdbSpecify 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(|I_{1}-kI_{2}|) / [ 0.5*sum(I_{1}+kI_{2}) ]`R1f`: sum(sqrt(I_{1})-sqrt(kI_{2})) / sum(sqrt(I_{1}))`R1i`: sum(|I_{1}-kI_{2}|) / sum(I_{1})`R2`: sqrt(sum[(I_{1}-kI_{2})^{2}] / sum(I_{1}^{2}))`CC`: The Pearson correlation coefficient.`CC*`: 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.

I

_{1}and I_{2}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.

This page was written by Thomas White.

Report bugs to taw@physics.org

Copyright © 2012-2020 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.

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/.

crystfel | check_hkl |

If CrystFEL is installed on your computer, you can read this manual page offline using the command `man compare_hkl`.