Update docs

10 files changed, 58 insertions, 44 deletions

diff --git a/doc/man/cell_explorer.1 b/doc/man/cell_explorer.1
index 79fdb83e..2e3594b7 100644
--- a/doc/man/cell_explorer.1
+++ b/doc/man/cell_explorer.1
@@ -27,6 +27,8 @@ Different colours are used to represent different centering types (P, A, B, C, I
 .P
 Click and drag with shift held down to select a range of values in one of the histograms.  Unit cells which have that parameter outside the selected range will be shown in grey in all the histograms.
 .P
+After selecting a range of values, use Tools->Fit Cell (or press Ctrl+F) to fit a normal distribution to the histogram data.  The mean and standard deviation of the parameter will be shown.  Unit cells will not be included in the fit if they are outside the ranges selected for the other parameters.
+.P
 The indexing algorithms found in the stream are shown as buttons at the top.  Click one of the buttons to deselect it, and again to select it again.  Unit cells from deselected algorithms will not be shown in the histograms (not even in grey).
 
 .SH AUTHOR
diff --git a/doc/man/check_hkl.1 b/doc/man/check_hkl.1
index 97787e3b..4c411d7d 100644
--- a/doc/man/check_hkl.1
+++ b/doc/man/check_hkl.1
@@ -39,12 +39,20 @@ Discard reflections with I/sigma(I) < \fIn\fR.  Default: -infinity (no cutoff).
 .PD 0
 .IP \fB--rmin=\fR\fI1/d\fR
 .PD
-Fix the lower resolution limit for the resolutions shells, as 1/d in m^-1.
+Low resolution cutoff, as 1/d in m^-1.  Use this or \fB--lowres\fR, but not both.
+
+.PD 0
+.IP \fB--lowres=\fR\fId\fR
+Low resolution cutoff in Angstroms.  Use this or \fB--rmin\fR, but not both.
 
 .PD 0
 .IP \fB--rmax=\fR\fI1/d\fR
 .PD
-Fix the upper resolution limit for the resolutions shells, as 1/d in m^-1.
+High resolution cutoff, as 1/d in m^-1.  Use this or \fB--highres\fR, but not both.
+
+.PD 0
+.IP \fB--highres=\fR\fId\fR
+High resolution cutoff in Angstroms.  Use this or \fB--rmax\fR, but not both.
 
 .PD 0
 .IP \fB--shell-file=\fR\fIfilename\fR
@@ -71,6 +79,10 @@ Ignore reflections with negative intensities.
 .PD
 Set to zero the intensities of reflections with negative intensities.
 
+.PD 0
+.IP \fB--nshells=\fIn\fR
+.PD
+Use \fIn\fR resolution shells.  Default: 10.
 
 .SH AUTHOR
 This page was written by Thomas White.
diff --git a/doc/man/compare_hkl.1 b/doc/man/compare_hkl.1
index 26ec7faf..1b4cdf4b 100644
--- a/doc/man/compare_hkl.1
+++ b/doc/man/compare_hkl.1
@@ -72,14 +72,14 @@ I1 and I2 are the intensities of the same reflection in both reflection lists.
 .RE
 
 .PD 0
-.IP \fB-u\fR
+.IP \fB--nshells=\fR\fIn\fR
 .PD
-Fix scale factors to unity.
+Use \fIn\fR resolution shells.  Default: 10.
 
 .PD 0
-.IP \fB--nshells=\fR\fIn\fR
+.IP \fB-u\fR
 .PD
-Use \fIn\fR resolution shells.  Default: 10.
+Fix scale factors to unity.
 
 .PD 0
 .IP \fB--shell-file=\fIfilename\fR
@@ -104,12 +104,20 @@ Discard reflections with I/sigma(I) < \fIn\fR.  Default: -infinity (no cutoff).
 .PD 0
 .IP \fB--rmin=\fR\fI1/d\fR
 .PD
-Discard reflections with lower than this value of 1/d in m^-1.
+Low resolution cutoff, as 1/d in m<sup>-1</sup>.  Use this or \fB--lowres\fR, but not both.
+
+.PD 0
+.IP \fB--lowres=\fR\fId\fR
+Low resolution cutoff in Angstroms.  Use this or \fB--rmin\fR, but not both.
 
 .PD 0
 .IP \fB--rmax=\fR\fI1/d\fR
 .PD
-Discard reflections with higher than this value of 1/d in m^-1.
+High resolution cutoff, as 1/d in m<sup>-1</sup>.  Use this or \fB--highres\fR, but not both.
+
+.PD 0
+.IP \fB--highres=\fR\fId\fR
+High resolution cutoff in Angstroms.  Use this or \fB--rmax\fR, but not both.
 
 .PD 0
 .IP \fB--intensity-shells\fR
@@ -118,12 +126,6 @@ Use intensity shells instead of resolution shells.  The range of shells will sta
 .sp
 Because of the hardcoded factor of 1/5000, needed to avoid a very uneven distribution of the number of reflection pairs in each bin, you are advised not to draw strong conclusions from the results of using this option.
 
-.PD 0
-.IP \fB--shell-file=\fR\fIfilename\fR
-.PD
-Write the statistics in resolution shells to \fIfilename\fR.
-
-
 .SH AUTHOR
 This page was written by Thomas White.
 
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5
index a8251578..f2745a93 100644
--- a/doc/man/crystfel_geometry.5
+++ b/doc/man/crystfel_geometry.5
@@ -1,7 +1,7 @@
 .\"
 .\" Geometry man page
 .\"
-.\" Copyright © 2012 Thomas White <taw@physics.org>
+.\" Copyright © 2012-2014 Thomas White <taw@physics.org>
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -106,7 +106,7 @@ The camera length (in metres) for this panel. You can also specify the HDF path
 .PD 0
 .IP \fBcoffset\fR
 .PD
-; The camera length offset (in metres) for this panel.  This number will be added to the camera length (\fBclen\fR).  This can be useful if the camera length is taken from the HDF5 file and you need to make an adjustment, such as that from a calibration experiment.
+The camera length offset (in metres) for this panel.  This number will be added to the camera length (\fBclen\fR).  This can be useful if the camera length is taken from the HDF5 file and you need to make an adjustment, such as that from a calibration experiment.
 
 .PD 0
 .IP \fBfs\fR
@@ -208,7 +208,7 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .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
diff --git a/doc/man/get_hkl.1 b/doc/man/get_hkl.1
index 0f310db8..1151f685 100644
--- a/doc/man/get_hkl.1
+++ b/doc/man/get_hkl.1
@@ -18,7 +18,7 @@ get_hkl \- manipulate reflection data
 .SH DESCRIPTION
 get_hkl performs various manipulations on reflection lists.  Possible manipulations include: expanding to a point group of lower symmetry, 'twinning' to a point group of higher symmetry, adding noise, restricting the list to contain only reflections included in another 'template' list, and some less common miscellaneous manipulations.
 .PP
-The input filename should be specified with \fB-i\fR \fIfilename\fR or \fB--input=\fR\fIfilename\fR.  The output filename should be specified with \fB-o\fR \fIfilename\fR or \fB--output=\fR\fIfilename\fR.  The symmetry of the input reflection list should be specified with \fB-y\fR \fIpointgroup\fR or \fB--symmetry=\fR\fIpointgroup\fR.  If you give the filename of a PDB file containing a CRYST1 line with unit cell parameters (using \fB-p\fR \fIfilename\fR or \fB--pdb=\fR\fIfilename\fR), the output reflection list will contain 1/d values.  Beyond these parameters, you can choose one of the manipulations described below.  The behaviour if multiple manipulations are requested is deliberately left undefined: it's much clearer to perform multiple manipulations in explicit separate steps.
+The input filename should be specified with \fB-i\fR \fIfilename\fR or \fB--input=\fR\fIfilename\fR.  The output filename should be specified with \fB-o\fR \fIfilename\fR or \fB--output=\fR\fIfilename\fR.  The symmetry of the input reflection list should be specified with \fB-y\fR \fIpointgroup\fR or \fB--symmetry=\fR\fIpointgroup\fR.  Beyond these parameters, you can choose one of the manipulations described below.  The behaviour if multiple manipulations are requested is deliberately left undefined: it's much clearer to perform multiple manipulations in explicit separate steps.
 
 .SH EXPANDING REFLECTIONS INTO A POINT GROUP OF LOWER SYMMETRY
 .PD 0
@@ -74,7 +74,13 @@ The intensities of the reflections will be multiplied by their symmetric multipl
 .IP \fB--cutoff-angstroms=\fR\fIn1,n2,n3\fR
 .PD
 In the first form, reflections with d (=lamba/2*sin(theta)) < \fIn\fR will be removed.
-In the second form, anisotropic truncation will be performed with separate resolution limits \fIn1\fR, \fIn2\fR and \fIn3\fR along a*, b* and c* respectively.
+In the second form, anisotropic truncation will be performed with separate resolution limits \fIn1\fR, \fIn2\fR and \fIn3\fR along a*, b* and c* respectively.  You must also specify \fB-p\fR or \fB--pdb\fR.
+
+.PD 0
+.IP \fB-p\fR \fIunitcell.pdb\fR
+.IP \fB--pdb=\fR\fIunitcell.pdb\fR
+.PD
+Specify the name of the PDB file containing at least a CRYST1 line describing the unit cell.
 
 .SH AUTHOR
 This page was written by Thomas White.
@@ -83,7 +89,7 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 get_hkl, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/hdfsee.1 b/doc/man/hdfsee.1
index a8c59fb6..da3a51f3 100644
--- a/doc/man/hdfsee.1
+++ b/doc/man/hdfsee.1
@@ -81,12 +81,12 @@ Use \fIscale\fR as the colour scale.  Possible scales are: \fBmono\fR, \fBinvmon
 .PD 0
 .IP \fB--median-filter=\fR\fIn\fR
 .PD
-Apply a median filter with box "radius" \fIn\fR to the image.  Each pixel will be set to the median of the values from a \fI(n+1)\fRx\fI(n+1)\fR square centered on the pixel.  This might help with peak detection if the background is high and/or noisy.  The \fIunfiltered\fR image will be used for the final integration of the peaks.  If you also use \fB--noise-filter\fR, the median filter will be applied first.
+Apply a median filter with box "radius" \fIn\fR to the image.  Each pixel will be set to the median of the values from a \fI(n+1)\fRx\fI(n+1)\fR square centered on the pixel.  If you also use \fB--noise-filter\fR, the median filter will be applied first.
 
 .PD 0
 .IP \fB--filter-noise\fR
 .PD
-Apply a noise filter to the image with checks 3x3 squares of pixels and sets all of them to zero if any of the nine pixels have a negative value.  This filter may help with peak detection under certain circumstances.  The \fIunfiltered\fR image will be used for the final integration of the peaks, because the filter is destroys a lot of information from the pattern.  If you also use \fB--median-filter\fR, the median filter will be applied first.
+Apply a noise filter to the image with checks 3x3 squares of pixels and sets all of them to zero if any of the nine pixels have a negative value.  If you also use \fB--median-filter\fR, the median filter will be applied first.
 
 .SH AUTHOR
 This page was written by Thomas White.
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index c0ddd41f..9133ecbb 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -34,23 +34,13 @@ folder a long way from the current directory, so you might want to specify a
 full pathname to be added in front of each filename.  You'll probably want to
 run more than one indexing job at a time (-j <n>).
 
-You can include a table of saturation values for in the HDF5 file, if you have
-a method for estimating the intensities of saturated peaks.  It goes in
-/processing/hitfinder/peakinfo_saturated, and should be an n*3 two dimensional
-array, where the first two columns contain fast scan and slow scan coordinates
-(in that order) and the third contains the value which should belong in a peak
-at the given location.  The value will be spread in a small cross centred on
-that location.
-
 See \fBman crystfel_geometry\fR for information about how to create a geometry description file and a beam parameters file.
 
 .SH PEAK DETECTION
 
 You can control the peak detection on the command line.  Firstly, you can choose the peak detection method using \fB--peaks=\fR\fImethod\fR.  Currently, two values for "method" are available.  \fB--peaks=hdf5\fR will take the peak locations from the HDF5 file.  It expects a two dimensional array at where size in the first dimension is the number of peaks and the size in the second dimension is three.  The first two columns contain the fast scan and slow scan coordinates, the third contains the intensity.  However, the intensity will be ignored since the pattern will always be re-integrated using the unit cell provided by the indexer on the basis of the peaks.  You can tell indexamajig where to find this table inside each HDF5 file using \fB--hdf5-peaks=\fR\fIpath\fR.
 
-If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search after Zaefferer (2000).  You can control the overall threshold and minimum squared gradient for finding a peak using \fB--threshold\fR and \fB--min-gradient\fR.  The threshold has arbitrary units matching the pixel values in the data, and the minimum gradient has the equivalent squared units.
-
-Peaks will be rejected if the 'foot point' is further away from the 'summit' of the peak by more than the inner integration radius (see below).  They will also be rejected if the peak is closer than twice the inner integration radius from another peak.
+If you use \fB--peaks=zaef\fR, indexamajig will use a simple gradient search after Zaefferer (2000).  You can control the overall threshold and minimum squared gradient for finding a peak using \fB--threshold\fR and \fB--min-gradient\fR.  The threshold has arbitrary units matching the pixel values in the data, and the minimum gradient has the equivalent squared units.  Peaks will be rejected if the 'foot point' is further away from the 'summit' of the peak by more than the inner integration radius (see below).  They will also be rejected if the peak is closer than twice the inner integration radius from another peak.
 
 You can suppress peak detection altogether for a panel in the geometry file by specifying the "no_index" value for the panel as non-zero.
 
@@ -335,7 +325,7 @@ Do not record integrated reflections in the stream.  The resulting output won't
 .PD 0
 .IP \fB--int-diag=\fIcondition\fR\fR
 .PD
-Show detailed information about reflection integration when \fIcondition\fR is met.  The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR, \fBimplausible\fR or \fBnegative\fR.  \fBrandom\fR means to show information about a random 1% of the peaks.  \fBnegative\fR means to show peaks with intensities which are negative my more than 3 sigma.  \fBimplausible\fR means to show peaks with intensities which are negative my more than 5 sigma.  The default is \fB--int-diag=none\fR.
+Show detailed information about reflection integration when \fIcondition\fR is met.  The \fIcondition\fR can be \fBall\fR, \fBnone\fR, a set of Miller indices separated by commas, \fBrandom\fR, \fBimplausible\fR or \fBnegative\fR.  \fBrandom\fR means to show information about a random 1% of the peaks.  \fBnegative\fR means to show peaks with intensities which are negative by more than 3 sigma.  \fBimplausible\fR means to show peaks with intensities which are negative by more than 5 sigma.  The default is \fB--int-diag=none\fR.
 
 .SH BUGS
 ReAx indexing is experimental.  It works very nicely for some people, and crashes for others.  In a future version, it will be improved and fully supported.
@@ -347,7 +337,7 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 indexamajig, and this manual, are part of CrystFEL.
 .P
@@ -360,5 +350,6 @@ You should have received a copy of the GNU General Public License along with Cry
 .SH SEE ALSO
 .BR crystfel (7),
 .BR crystfel_geometry (5),
+.BR cell_explorer (1),
 .BR process_hkl (1),
 .BR partialator (1)
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index 9e74b97b..db615dac 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -114,7 +114,7 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012-2013 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 partial_sim, and this manaul, are part of CrystFEL.
 .P
diff --git a/doc/man/partialator.1 b/doc/man/partialator.1
index b3871ed7..c209b97d 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -1,7 +1,7 @@
 .\"
 .\" partialator man page
 .\"
-.\" Copyright © 2012 Thomas White <taw@physics.org>
+.\" Copyright © 2012-2014 Thomas White <taw@physics.org>
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -38,7 +38,7 @@ considered ready for processing experimental data.
 .IP "\fB-i\fR \fIfilename\fR"
 .IP \fB--input=\fR\fIfilename\fR
 .PD
-Give the name of the input stream..
+Give the name of the input stream.
 
 .PD 0
 .IP "\fB-o\fR \fIfilename\fR"
@@ -110,7 +110,7 @@ point, and the part of reciprocal space excited by the Ewald sphere taking into
 account the finite bandwidth and convergence angle.  A Lorentz factor will also
 be used, proportional to the distance between the limiting Ewald spheres.
 
-For a fully description including diagrams, see T. A. White et al., Acta Cryst.
+For a full description including diagrams, see T. A. White et al., Acta Cryst.
 D69 (2013) p1231-1240.
 
 .IP \fBunity\fR
@@ -133,7 +133,7 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 partialator, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/process_hkl.1 b/doc/man/process_hkl.1
index 427e3b75..e4a3dd8f 100644
--- a/doc/man/process_hkl.1
+++ b/doc/man/process_hkl.1
@@ -1,7 +1,7 @@
 .\"
 .\" process_hkl man page
 .\"
-.\" Copyright © 2012 Thomas White <taw@physics.org>
+.\" Copyright © 2012-2014\f Thomas White <taw@physics.org>
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -122,7 +122,7 @@ 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.
+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.
 
 .SH AUTHOR
 This page was written by Thomas White.
@@ -131,9 +131,9 @@ This page was written by Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2012 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2014 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
-process_hkl, and this manual, are part of CrystFEL.
+qprocess_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
@@ -147,4 +147,5 @@ You should have received a copy of the GNU General Public License along with Cry
 .BR compare_hkl (1),
 .BR check_hkl (1),
 .BR render_hkl (1),
+.BR ambigator (1),
 .BR partialator (1)