19 files changed, 110 insertions, 68 deletions
diff --git a/doc/man/ambigator.1 b/doc/man/ambigator.1
index fad89641..65ef16a0 100644
--- a/doc/man/ambigator.1
+++ b/doc/man/ambigator.1
@@ -1,7 +1,7 @@
 .\"
 .\" ambigator man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -111,7 +111,7 @@ 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 © 2014-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2014-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 
 ambigator, and this manual, are part of CrystFEL.
 
diff --git a/doc/man/cell_explorer.1 b/doc/man/cell_explorer.1
index 990a9108..1ce12217 100644
--- a/doc/man/cell_explorer.1
+++ b/doc/man/cell_explorer.1
@@ -1,7 +1,7 @@
 .\"
 .\" cell_explorer man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -38,7 +38,7 @@ 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 © 2014-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2014-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 cell_explorer, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/check_hkl.1 b/doc/man/check_hkl.1
index f02b581b..71cba848 100644
--- a/doc/man/check_hkl.1
+++ b/doc/man/check_hkl.1
@@ -1,7 +1,7 @@
 .\"
 .\" check_hkl man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -93,7 +93,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 check_hkl, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/compare_hkl.1 b/doc/man/compare_hkl.1
index 30fcd93e..f85f6c90 100644
--- a/doc/man/compare_hkl.1
+++ b/doc/man/compare_hkl.1
@@ -1,7 +1,7 @@
 .\"
 .\" compare_hkl man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -139,7 +139,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 compare_hkl, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/crystfel.7 b/doc/man/crystfel.7
index b7063b21..7ed67d5b 100644
--- a/doc/man/crystfel.7
+++ b/doc/man/crystfel.7
@@ -1,7 +1,7 @@
 .\"
 .\" CrystFEL main man page
 .\"
-.\" Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -142,7 +142,7 @@ Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>
 
 .SH COPYRIGHT AND DISCLAIMER
 .PD 0
-Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .PD
 .PP
 Please read the AUTHORS file in the CrystFEL source code distribution for a full list of contributions and contributors.
diff --git a/doc/man/crystfel_geometry.5 b/doc/man/crystfel_geometry.5
index 47ca5138..cf64d76e 100644
--- a/doc/man/crystfel_geometry.5
+++ b/doc/man/crystfel_geometry.5
@@ -1,7 +1,7 @@
 .\"
 .\" Geometry man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -294,7 +294,7 @@ This page was written by Thomas White and Valerio Mariani.
 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.
+Copyright © 2012-2018 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/geoptimiser.1 b/doc/man/geoptimiser.1
index e2370c7e..369a36f1 100644
--- a/doc/man/geoptimiser.1
+++ b/doc/man/geoptimiser.1
@@ -1,7 +1,7 @@
 .\"
 .\" geoptimiser man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -139,7 +139,7 @@ This page was written by Valerio Mariani, Oleksandr Yefanov and Thomas White.
 Report bugs to <taw@physics.org>, or visit <http://www.desy.de/~twhite/crystfel>.
 
 .SH COPYRIGHT AND DISCLAIMER
-Copyright © 2014-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2014-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 geoptimiser, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/get_hkl.1 b/doc/man/get_hkl.1
index a5480e20..90637a8a 100644
--- a/doc/man/get_hkl.1
+++ b/doc/man/get_hkl.1
@@ -1,7 +1,7 @@
 .\"
 .\" get_hkl man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -96,7 +96,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 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 8d5cccb5..3034d032 100644
--- a/doc/man/hdfsee.1
+++ b/doc/man/hdfsee.1
@@ -1,7 +1,7 @@
 .\"
 .\" hdfsee man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -112,7 +112,7 @@ This page was written by Thomas White and Valerio Mariani.
 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.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 hdfsee, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/indexamajig.1 b/doc/man/indexamajig.1
index 3f49701f..c0fe8277 100644
--- a/doc/man/indexamajig.1
+++ b/doc/man/indexamajig.1
@@ -1,7 +1,7 @@
 .\"
 .\" indexamajig man page
 .\"
-.\" Copyright © 2012-2017 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -89,7 +89,7 @@ You can add one or more of the following to the above indexing methods, to contr
 
 .IP \fB-latt\fR
 .PD
-Provide the Bravais lattice type (e.g. the knowledge that the lattice tetragonal primitive), as prior information to the indexing engine.
+Provide the Bravais lattice type (e.g. the knowledge that the lattice is tetragonal primitive), as prior information to the indexing engine.
 
 .IP \fB-nolatt\fR
 .PD
@@ -101,7 +101,7 @@ Provide your unit cell parameters as prior information to the indexing engine.
 
 .IP \fB-nocell\fR
 .PD
-The opposite of \fB-cell\fR: do not use unit cell parameters as prior information for the core indexing algorithm.
+The opposite of \fB-cell\fR: do not provide unit cell parameters as prior information to the indexing engine.
 
 .PP
 Example: \fB--indexing=mosflm-cell-latt\fR means to use Mosflm for indexing, and provide it with unit cell parameters and Bravais lattice type information.
@@ -112,7 +112,7 @@ The default indexing method is 'none', which means no indexing will be done.  Th
 .PP
 You do not need to explicitly specify anything more than the indexing method itself (e.g. \fBmosflm\fR or \fBasdf\fR).  The default behaviour for all indexing methods is to make the maximum possible use of prior information such as the lattice type and cell parameters.  If you do not provide this information, for example if you do not give any unit cell file or if the unit cell file does not contain cell parameters (only lattice type information), the indexing methods you give will be modified accordingly.  If you only specify the indexing methods themselves, in most cases \fBindexamajig\fR will do what you want and intuitively expect!  However, the options are available if you need finer control.
 
-If you don't know what to give for this option, try \fB--indexing=asdf,dirax,mosflm,xds,taketwo\fR.
+If you don't know what to give for this option, leave it out completely.  Indexamajig will then automatically select indexing methods based on the programs available on your computer.
 
 The indexing results from the indexing engine will be put through a number of refinement and checking stages.  See the options \fB--no-check-cell, --no-cell-combinations, --no-multi, --no-retry\fR and \fB--no-refine\fR below for more details.
 
@@ -305,7 +305,7 @@ With this option with \fB--peaks=hdf5\fR, the peaks will additionally be checked
 .PD 0
 .IP \fB--indexing=\fR\fImethod\fR
 .PD
-Index the patterns using \fImethod\fR.  See the section titled \fBINDEXING METHODS\fR (above) for more information.  The default is \fB--indexing=none\fR.
+Index the patterns using \fImethod\fR.  See the section titled \fBINDEXING METHODS\fR (above) for more information.  The default is to automatically detect which indexing methods to use.
 
 .PD 0
 .IP "\fB-p\fR \fIunitcell.cell\fR"
@@ -332,9 +332,9 @@ Do not check the cell parameters against the reference unit cell (given with \fB
 When checking the cell parameters against the reference cell (see \fB-p\fR), do not make combinations of the axes of the candidate cell (such as \fBa'\fR=2\fBa\fR+\fBb\fR) to make it fit.  Usually this reduces the success rate, but is necessary if one of the cell parameters is close to a multiple of the others.  \fRThis happens for tetragonal lysozyme\fB.
 
 .PD 0
-.IP \fB--no-multi
+.IP \fB--multi
 .PD
-Disable multi-lattice indexing.  This refers to the "subtract and retry" method, where after a successful indexing attempt the spots accounted for by the indexing solution are removed before trying to index again in the hope of finding a second lattice.  This doesn't have anything to do with the multi-lattice indexing algorithms such as Felix.
+Enable the "subtract and retry" method, where after a successful indexing attempt the spots accounted for by the indexing solution are removed before trying to index again in the hope of finding a second lattice.  This doesn't have anything to do with the multi-lattice indexing algorithms such as Felix.
 
 .PD 0
 .IP \fB--no-retry
@@ -501,7 +501,7 @@ 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 © 2012-2017 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 indexamajig, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/list_events.1 b/doc/man/list_events.1
index 900288f6..5ce086d1 100644
--- a/doc/man/list_events.1
+++ b/doc/man/list_events.1
@@ -1,8 +1,8 @@
 .\"
 .\" list_events man page
 .\"
-.\" Copyright © 2015 Deutsches Elektronen-Synchrotron DESY,
-.\"                   a research centre of the Helmholtz Association.
+.\" Copyright © 2015-2018 Deutsches Elektronen-Synchrotron DESY,
+.\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -43,7 +43,7 @@ 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 © 2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2015-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 list_events, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/partial_sim.1 b/doc/man/partial_sim.1
index 88148776..72655758 100644
--- a/doc/man/partial_sim.1
+++ b/doc/man/partial_sim.1
@@ -1,7 +1,7 @@
 .\"
 .\" partial_sim man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -155,7 +155,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 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 decaa07c..aa25d2a7 100644
--- a/doc/man/partialator.1
+++ b/doc/man/partialator.1
@@ -1,7 +1,7 @@
 .\"
 .\" partialator man page
 .\"
-.\" Copyright © 2012-2016 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -132,29 +132,45 @@ Reject crystals if the absolute values of their relative Debye-Waller ("B") fact
 .PD
 Write out the per-crystal parameters and reflection lists after every cycle of refinement, instead of only at the end.  The intermediate reflection lists and parameter filenames will be prefixed with \fBiter\fIN\fB_\fR (note the trailing underscore), where \fIN\fR is the iteration number.  If you use \fB--custom-split\fR, intermediate results will also be output for each custom dataset.
 
+.PD 0
+.IP \fB--no-logs\fR
+.PD
+Do not write the extensive log files needed for plotting contour maps and spectrum graphs.  This makes the process a lot faster, but you probably do want these logs to check that post-refinement is working reasonably.
+
+.PD 0
+.IP "\fB-w\fR \fIpg\fR"
+.PD
+Set the apparent symmetry of the crystals.  The ambiguity operator will be determined by comparing this to the actual symmetry.
+.IP
+If you prefer (or the scenario demands it), you can specify the ambiguity operator directly using \fB--operator\fR.
+
+.PD 0
+.IP \fB--operator=\fR\fIop\fR
+.PD
+Specify the indexing ambiguity operator.  Example: \fB--operator=k,h,-l\fR.
+.IP
+If you prefer, you can specify the ambiguity operator by specifying the apparent symmetry using \fB-w\fR.
+
+.PD 0
+.IP \fB--force-bandwidth=\fIbw\fR
+.IP \fB--force-radius=\fIR\fR
+.PD
+Set the X-ray bandwidth or initial profile radius for all crystals before proceeding, overriding the values from the stream.  Bandwidth is given as a fraction, i.e. \fB--force-bandwidth=0.0013\fR means 0.13 percent (approximate FWHM).  Radius is given in  nm^-1.
+
 .SH PARTIALITY MODELS
 
 The available partiality models are:
 
-.IP \fBscsphere\fR
+.IP \fBxsphere\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.
+source for the reflection.  The X-ray spectrum is modelled as a super-Gaussian
+with exponent 1.5, and the overlap integral is evaluated numerically.
 
-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.
+This model is the same as that described in Acta Cryst. D71 (2015) p1400.
 
 .IP \fBunity\fR
 .PD
@@ -174,15 +190,15 @@ partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=uni
 
 .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
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --iterations=0\fR
 
 .IP "Merging with partialities, with scaling but without post-refinement:"
 .PD
-partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scsphere --iterations=1 --no-pr\fR
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --iterations=1 --no-pr\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
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --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)
 
@@ -190,11 +206,9 @@ partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=scs
 .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
+partialator -i \fImy.stream \fR-o \fImy.hkl\fR -y \fImypointgroup \fB--model=xsphere --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 CUSTOM DATASET SPLITTING
 When performing a time-resolved experiment (for example), it is preferable to ensure that the data for all time points has been processed identically.  Rather than processing each time point independently with separate runs of partialator, it is better to process them all together and do the splitting into time points just before the final output.  Consider, for example, the case of simple scaling (without a B factor): when merging independently, the resulting datasets would probably end up with different overall scaling factors.  When comparing the results, you would need to take this difference into account.  In practice, most programs can do that job easily, but what about if a B factor is included?  And what if partialities are included - how unique is the solution?
@@ -216,7 +230,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 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/pattern_sim.1 b/doc/man/pattern_sim.1
index 7c761c71..c93c5e4c 100644
--- a/doc/man/pattern_sim.1
+++ b/doc/man/pattern_sim.1
@@ -1,7 +1,7 @@
 .\"
 .\" pattern_sim man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -246,7 +246,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 pattern_sim, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/process_hkl.1 b/doc/man/process_hkl.1
index 3876005a..658f42bf 100644
--- a/doc/man/process_hkl.1
+++ b/doc/man/process_hkl.1
@@ -1,7 +1,7 @@
 .\"
 .\" process_hkl man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -141,7 +141,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 qprocess_hkl, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/render_hkl.1 b/doc/man/render_hkl.1
index eadbba34..a7e67442 100644
--- a/doc/man/render_hkl.1
+++ b/doc/man/render_hkl.1
@@ -1,7 +1,7 @@
 .\"
 .\" render_hkl man page
 .\"
-.\" Copyright © 2012-2015 Deutsches Elektronen-Synchrotron DESY,
+.\" Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY,
 .\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
@@ -125,7 +125,7 @@ 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 © 2012-2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2012-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 render_hkl, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/man/whirligig.1 b/doc/man/whirligig.1
index e213a007..938ac5d0 100644
--- a/doc/man/whirligig.1
+++ b/doc/man/whirligig.1
@@ -1,8 +1,8 @@
 .\"
 .\" whirligig man page
 .\"
-.\" Copyright © 2015 Deutsches Elektronen-Synchrotron DESY,
-.\"                  a research centre of the Helmholtz Association.
+.\" Copyright © 2015-2018 Deutsches Elektronen-Synchrotron DESY,
+.\"                       a research centre of the Helmholtz Association.
 .\"
 .\" Part of CrystFEL - crystallography with a FEL
 .\"
@@ -38,7 +38,7 @@ 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 © 2015 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
+Copyright © 2015-2018 Deutsches Elektronen-Synchrotron DESY, a research centre of the Helmholtz Association.
 .P
 whirligig, and this manual, are part of CrystFEL.
 .P
diff --git a/doc/reference/libcrystfel/CrystFEL-docs.sgml b/doc/reference/libcrystfel/CrystFEL-docs.sgml
index c6131ae7..15d9f43f 100644
--- a/doc/reference/libcrystfel/CrystFEL-docs.sgml
+++ b/doc/reference/libcrystfel/CrystFEL-docs.sgml
@@ -8,7 +8,7 @@
   <bookinfo>
     <title>CrystFEL Reference Manual</title>
     <releaseinfo>
-      For libcrystfel from CrystFEL 0.6.3.
+      For libcrystfel from CrystFEL 0.7.0.
     </releaseinfo>
     <abstract>
     This is the internal documentation for CrystFEL.  Unless you are looking at
diff --git a/doc/reference/libcrystfel/CrystFEL-sections.txt b/doc/reference/libcrystfel/CrystFEL-sections.txt
index 206ba4df..4a436e34 100644
--- a/doc/reference/libcrystfel/CrystFEL-sections.txt
+++ b/doc/reference/libcrystfel/CrystFEL-sections.txt
@@ -15,7 +15,9 @@ add_refl
 add_refl_to_list
 <SUBSECTION>
 first_refl
+first_refl_const
 next_refl
+next_refl_const
 <SUBSECTION>
 find_refl
 next_found_refl
@@ -24,7 +26,6 @@ get_detector_pos
 get_panel
 get_partiality
 get_lorentz
-get_partial
 get_indices
 get_symmetric_indices
 get_intensity
@@ -36,12 +37,14 @@ get_peak
 get_temp1
 get_temp2
 get_flag
+get_exerr
+get_khalf
+get_kpred
 <SUBSECTION>
 set_detector_pos
 set_panel
 set_partiality
 set_lorentz
-set_partial
 set_intensity
 set_redundancy
 set_esd_intensity
@@ -52,6 +55,9 @@ set_symmetric_indices
 set_temp1
 set_temp2
 set_flag
+set_exerr
+set_khalf
+set_kpred
 <SUBSECTION>
 copy_data
 num_reflections
@@ -130,6 +136,7 @@ rotate_cell
 cell_print
 resolution
 match_cell
+compare_cells
 match_cell_ab
 cell_is_sensible
 validate_cell
@@ -143,6 +150,7 @@ load_cell_from_file
 write_cell
 lattice_from_str
 cell_get_volume
+transform_cell_gsl
 </SECTION>
 
 <SECTION>
@@ -228,6 +236,7 @@ imagefile_get_type
 imagefile_open
 imagefile_read
 imagefile_read_simple
+is_cbf_file
 <SUBSECTION>
 new_imagefile_field_list
 add_imagefile_field
@@ -276,34 +285,48 @@ stat_scale_intensity
 <FILE>indexing</FILE>
 IndexingMethod
 IndexingPrivate
+IndexingFlags
 INDEXING_DEFAULTS_DIRAX
 INDEXING_DEFAULTS_MOSFLM
 INDEXING_DEFAULTS_XDS
 INDEXING_DEFAULTS_ASDF
 INDEXING_DEFAULTS_FELIX
+INDEXING_DEFAULTS_TAKETWO
 INDEXING_METHOD_MASK
-INDEXING_CONTROL_FLAGS
+detect_indexing_methods
 setup_indexing
 cleanup_indexing
 get_indm_from_string
+get_indm_from_string_2
 index_pattern
 index_pattern_2
 indexer_str
+dirax_probe
 dirax_prepare
 run_dirax
 dirax_cleanup
+mosflm_probe
 mosflm_prepare
 run_mosflm
 mosflm_cleanup
+xds_probe
 xds_prepare
 run_xds
 xds_cleanup
+asdf_probe
 asdf_prepare
 run_asdf
 asdf_cleanup
+felix_options
+felix_probe
 felix_prepare
 felix_index
 felix_cleanup
+taketwo_options
+taketwo_probe
+taketwo_prepare
+taketwo_index
+taketwo_cleanup
 </SECTION>
 
 <SECTION>
@@ -470,6 +493,7 @@ crystal_copy
 crystal_free
 <SUBSECTION>
 crystal_get_cell
+crystal_get_cell_const
 crystal_get_image
 crystal_get_mosaicity
 crystal_get_num_saturated_reflections
@@ -502,9 +526,9 @@ crystal_set_det_shift
 <FILE>geometry</FILE>
 PartialityModel
 gparam
-find_intersections
-find_intersections_to_res
-update_partialities
+predict_to_res
+update_predictions
+calculate_partialities
 polarisation_correction
 sphere_fraction
 gaussian_fraction
@@ -547,6 +571,7 @@ integrate_all
 integrate_all_2
 integrate_all_3
 integrate_all_4
+integrate_all_5
 integration_method
 </SECTION>
 
@@ -571,6 +596,7 @@ open_stream_for_read
 open_stream_for_write
 open_stream_for_write_2
 open_stream_for_write_3
+open_stream_for_write_4
 get_stream_fd
 close_stream
 read_chunk
@@ -582,6 +608,8 @@ is_stream
 write_command
 write_geometry_file
 stuff_from_stream
+stream_audit_info
+stream_has_old_indexers
 </SECTION>
 
 <SECTION>