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.\"
.\" partialator man page
.\"
.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
.\" a research centre of the Helmholtz Association.
.\"
.\" Part of CrystFEL - crystallography with a FEL
.\"
.TH PARTIALATOR 1
.SH NAME
partialator \- scaling and post-refinement of partial reflections
.SH SYNOPSIS
.PP
.B partialator
\fB-i\fR \fIinput.stream\fR
\fB-o\fR \fIoutput.hkl\fR
\fB-y\fR \fIpointgroup\fR
[\fBoptions\fR] \fB...\fR
.PP
.B partialator
\fB--help\fR
.SH DESCRIPTION
\fBpartialator\fR merges reflections by scaling and post refinement, accounting
for the partialities of the reflections. That means that it models the geometry
of diffraction for each pattern (crystal orientation, unit cell parameters,
X-ray bandwidth and so on) and attempts to optimise the geometrical parameters
to make the fully integrated intensities calculated using the model agree as
closely as possible between the many patterns.
See USAGE CASES below for examples of commands to merge reflections in different
ways, for example with and without partiality or scaling.
In addition to the output reflection list, \fBpartialator\fR will write a file called partialator.params which contains the scaling factors determined for each crystal. After each iteration, a file will be written called pgraph-iter\fIn\fR.dat which contains the observed and calculated partialities for a randomly chosen set of "free" reflections which were not included in the refinement.
.SH OPTIONS
.PD 0
.IP "\fB-i\fR \fIfilename\fR"
.IP \fB--input=\fR\fIfilename\fR
.PD
Give the name of the input stream.
.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=partialator.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-n\fR \fIn\fR"
.IP \fB--iterations=\fR\fIn\fR
.PD
Run \fIn\fR cycles of scaling and post refinement.
.PD 0
.IP \fB--no-scale\fR
.PD
Fix all the overall scaling factors to be unity.
.PD 0
.IP "\fB-m\fR \fImodel\fR"
.IP \fB--model=\fR\fImodel\fR
.PD
Specify the partiality model. See the list below for possible choices.
.PD 0
.IP "\fB-j\fR \fIn\fR"
.PD
Run \fIn\fR analyses in parallel.
.PD 0
.IP \fB--no-polarisation\fR
.PD
Disable the polarisation correction.
.PD 0
.IP \fB--max-adu=\fR\fIn\fR
.PD
Include reflections only if their peak values were less than \fIn\fR. That means, \fIn\fR is the saturation value of the detector. The default is infinity, i.e. no cutoff.
.PD 0
.IP \fB--min-measurements=\fR\fIn\fR
.PD
Include a reflection in the output only if it appears at least least \fIn\fR times. The default is \fB--min-measurements=2\fR.
.PD 0
.IP \fB--push-res=\fIn\fR
.PD
Merge reflections which are up to \fIn\fR nm^-1 higher than the apparent resolution limit of each individual crystal. \fIn\fR can be negative to merge \fIlower\fR than the apparent resolution limit. The default is \fBpush-res=0\fR - note that this is different to the default behaviour of \fBprocess_hkl\fR.
.PD 0
.IP \fB--start-after=\fR\fIn\fR
.PD
Ignore the first \fIn\fR crystals in the input. The default is \fB--start-after=0\fR, i.e. start at the beginning.
.PD 0
.IP \fB--stop-after=\fR\fIn\fR
.PD
Stop processing after \fIn\fR crystals have been successfully read. The default is \fB--stop-after=0\fR, which means to process all the patterns from the start point to the end of the input (see \fB--start-after\fR).
.SH PARTIALITY MODELS
The available partiality models are:
.IP \fBscsphere\fR
.PD
The volume of intersection between a sphere centered on each reciprocal lattice
point and the part of reciprocal space excited by the Ewald sphere taking into
account the finite bandwidth and convergence angle. A "source coverage factor"
is included to take into account the spectral brightness of the effective
source for the reflection.
This model is similar to that described in Acta Cryst. D69 (2013) p1231-1240,
and in Phil. Trans. Roy. Soc. B 369 (2014) 20130330, except that the "Lorentz
factor" described there is no longer treated as a separate factor.
.IP \fBscgaussian\fR
.PD
As \fBscsphere\fR, except that the shape of the scattering density centered on
each reciprocal lattice point is taken to be a 3D Gaussian distribution instead
of a sphere. The standard deviation of the distribution will be the profile
radius (determined by indexamajig) divided by 2.6.
.IP \fBunity\fR
.PD
Fix all partialities at 1.
.SH USAGE CASES
.IP "Merging without scaling, partialities or post-refinement:"
.PD
partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=unity --iterations=0\fR
.IP "Merging without partialities or post-refinement, but with scaling:"
.PD
partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=unity --iterations=1\fR
.IP
(Use a higher number of iterations to increase the accuracy of scaling, but at a cost of more CPU time and possibly more rejected crystals)
.IP "Merging with partialities, but without post-refinement and without scaling:"
.PD
partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=0\fR
.IP "Merging with partialities, post-refinement and scaling:"
.PD
partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1\fR
.IP
(Use a higher number of iterations to increase the accuracy of scaling and post-refinement, but at a cost of more CPU time and possibly more rejected crystals)
.IP "Merging with partialities and post-refinement, but without scaling:"
.PD
This would be a strange thing to want to do, however:
.IP
partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1 --no-scale\fR
.IP
(Use a higher number of iterations to increase the accuracy of post-refinement, but at a cost of more CPU time and possibly more rejected crystals)
.PP
\fBscguassian\fR could be substituted for \fBscsphere\fR in the above examples to use the Gaussian partiality model instead of the spherical one.
.SH AUTHOR
This page was written by Thomas White.
.SH REPORTING BUGS
Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
.SH COPYRIGHT AND DISCLAIMER
Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
.P
partialator, 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 <http://www.gnu.org/licenses/>.
.SH SEE ALSO
.BR crystfel (7),
.BR indexamajig (1),
.BR process_hkl (1),
.BR partial_sim (1)
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