.\" .\" process_hkl man page .\" .\" Copyright © 2012 Thomas White .\" .\" Part of CrystFEL - crystallography with a FEL .\" .TH PROCESS_HKL 1 .SH NAME process_hkl \- Monte Carlo merging of Bragg intensities .SH SYNOPSIS .PP .B process_hkl \fB-i\fR \fImypatterns.stream\fR \fB-o\fR \fImydata.hkl\fR \fB-y\fR \fIpointgroup\fR [\fBoptions\fR] \fB...\fR .PP .B process_hkl \fB--help\fR .SH DESCRIPTION process_hkl takes a data stream, such as that from \fBindexamajig\fR, and merges the many individual intensities together to form a single list of reflection intensities which are useful for crystallography. Merging is done by the Monte Carlo method, otherwise known as taking the mean of the individual values. .SH OPTIONS .PD 0 .IP "\fB-i\fR \fIfilename\fR" .IP \fB--input=\fR\fIfilename\fR .PD Give the name of the input stream. \fB--input=-\fR means to use stdin. .PD 0 .IP "\fB-o\fR \fIfilename\fR" .IP \fB--output=\fR\fIfilename\fR .PD Give the name of the output file. The default is \fB--output=processed.hkl\fR. .PD 0 .IP "\fB-y\fR \fIpointgroup\fR" .IP \fB--symmetry=\fR\fIpointgroup\fR .PD Merge according to symmetry \fIpointgroup\fR. .PD 0 .IP "\fB-g\fR \fIh,k,l\fR" .IP \fB--histogram=\fR\fIh,k,l\fR .PD Calculate a histogram of intensities for \fIh,k,l\fR, which will be written as \fBhistogram.dat\fR in the current directory. .PD 0 .IP "\fB-z\fR \fImin,max,nbins\fR" .IP \fB--hist-parameters=\fR\fImin,max,nbins\fR .PD Set the minimum and maximum values, and the number of bins, to \fImin\fR, \fImax\fR and \fInbins\fR, respectively. .PD 0 .IP \fB--start-after=\fR\fIn\fR .PD Ignore the first \fIn\fR patterns in the stream. .PD 0 .IP \fB--stop-after=\fR\fIn\fR .PD Stop after processing \fIn\fR patterns. .PD 0 .IP \fB--start-after=\fR\fIn\fR .PD Ignore the first \fIn\fR patterns in the stream, not including those skipped with \fB--start-after\fR, if any. .PD 0 .IP \fB--reference=\fR\fIfilename\fR .PD Use intensities from \fIfilename\fR as the reference when scaling, instead of the current model. .PD 0 .IP \fB--scale\fR .PD Attempt to scale each pattern for best fit with the current model. Scaling using process_hkl doesn't work very well: use \fBpartialator\fR if you need more advanced merging techniques. .PD 0 .IP \fB--sum\fR .PD Sum the intensities, instead of averaging them. This might be useful for comparing results to radially summed powder patterns, but usually gives less useful final intensities. \fBpowder_plot\fR has more advanced features for calculating 'powder' patterns. .PD 0 .IP \fB--max-only\fR .PD Output the maximum intensity for each reflection rather than the mean value of all intensities. This is usually not useful. .PD 0 .IP \fB--no-polarisation\fR .PD Disable the polarisation correction. .SH CHOICE OF POINT GROUP FOR MERGING One of the main features of serial crystallography is that the orientations of individual crystals are random. That means that the orientation of each crystal must be determined independently, with no information about its relationship to the orientation of crystals in other patterns. Some symmetry classes are merohedral, which means that they have lower symmetry than their lattices. This means that the orientation determined by indexing will have an ambiguity. In such cases, you will need to merge according to corresponding holohedral point group. To determine what this is, consult the tables in \fRtwin-calculator.pdf\fB. For further information, see the theory page of the CrystFEL website. .SH AUTHOR This page was written by Thomas White. .SH REPORTING BUGS Report bugs to , or visit . .SH COPYRIGHT AND DISCLAIMER Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association. .P process_hkl, and this manual, are part of CrystFEL. .P 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. .P 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. .P You should have received a copy of the GNU General Public License along with CrystFEL. If not, see . .SH SEE ALSO .BR crystfel (7), .BR indexamajig (5), .BR compare_hkl (1), .BR check_hkl (1), .BR render_hkl (1), .BR powder_plot (1), .BR partialator (1)